From de39d5a04f8b3361f7283a529b4670df1dd26fac Mon Sep 17 00:00:00 2001
From: jhudsl-robot <itcrtrainingnetwork@gmail.com>
Date: Fri, 2 Feb 2024 19:11:06 +0000
Subject: [PATCH] Render bookdown

---
 docs/02-research_team.md        |  13 +-
 docs/404.html                   | 102 +++++-----
 docs/about-the-authors.html     | 102 +++++-----
 docs/anvil-workspace.html       | 120 ++++++------
 docs/background.html            | 102 +++++-----
 docs/billing.html               | 144 +++++++-------
 docs/data-1.html                | 128 +++++++------
 docs/index.html                 | 102 +++++-----
 docs/instructor-guide.html      | 112 +++++------
 docs/programming-platforms.html | 180 +++++++++---------
 docs/reference-keys.txt         |   2 +
 docs/references.html            | 112 +++++------
 docs/research-team.html         | 116 ++++++-----
 docs/search_index.json          |   2 +-
 docs/student-guide.html         | 164 ++++++++--------
 docs/support.html               | 328 ++++++++++++++++++++++++++++++++
 16 files changed, 1103 insertions(+), 726 deletions(-)
 create mode 100644 docs/support.html

diff --git a/docs/02-research_team.md b/docs/02-research_team.md
index 09cfec8..0458c08 100644
--- a/docs/02-research_team.md
+++ b/docs/02-research_team.md
@@ -26,10 +26,19 @@ Soil sampling for this project was done by both faculty and student volunteers f
 - **Petersburg, VA**: Virginia State University
 - **Seattle, WA**: North Seattle College, Pierce College
 - **Tsaile, AZ**: Din&eacute; College  
-  
+
+
+# Support
+
+This project would not be possible without financial and technical support from many organizations and people. 
+
 ## Funding
   
-Funding for this project has been provided by the [National Human Genome Research Institute](https://www.genome.gov/) (Contract # 75N92022P00232 awarded to Johns Hopkins University), as well as by donations from [PacBio](https://www.pacb.com/) and [CosmosID](https://www.cosmosid.com/).
+Funding for this project has been provided by the [National Human Genome Research Institute](https://www.genome.gov/) (Contract # 75N92022P00232 awarded to Johns Hopkins University). 
+
+## Sponsors
+
+[PacBio](https://www.pacb.com/) and [CosmosID](https://www.cosmosid.com/) have graciously donated supplies.
 
 [Advances in Genome Biology and Technology](https://www.agbt.org/) provided funding support for several team members to attend AGBT 2024.
 
diff --git a/docs/404.html b/docs/404.html
index 53c1538..869aeaa 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -123,81 +123,85 @@
 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
-<li class="chapter" data-level="2.2" data-path="research-team.html"><a href="research-team.html#funding"><i class="fa fa-check"></i><b>2.2</b> Funding</a></li>
-<li class="chapter" data-level="2.3" data-path="research-team.html"><a href="research-team.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>2.3</b> Analytical and Computational Support</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
+<li class="chapter" data-level="3" data-path="support.html"><a href="support.html"><i class="fa fa-check"></i><b>3</b> Support</a>
 <ul>
-<li class="chapter" data-level="3.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>3.1</b> Sample Metadata</a></li>
-<li class="chapter" data-level="3.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>3.2</b> Soil Testing Data</a></li>
-<li class="chapter" data-level="3.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>3.3</b> Genomics and Metagenomics Data</a></li>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
 </ul></li>
 <li class="part"><span><b>Using AnVIL</b></span></li>
-<li class="chapter" data-level="4" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>4</b> Billing</a>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
 <ul>
-<li class="chapter" data-level="4.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>4.1</b> Create Google Billing Account</a></li>
-<li class="chapter" data-level="4.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>4.2</b> Add Terra to Google Billing Account</a></li>
-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
-<li class="chapter" data-level="4.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>4.4</b> Set Alerts for Google Billing</a></li>
-<li class="chapter" data-level="4.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>4.5</b> View Spend for Google Billing</a></li>
-<li class="chapter" data-level="4.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>4.6</b> Create Terra Billing Project</a></li>
-<li class="chapter" data-level="4.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>4.7</b> Add Member to Terra Billing Project</a></li>
-<li class="chapter" data-level="4.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>4.8</b> Disable Terra Billing Project</a></li>
+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
 </ul></li>
-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>6.4</b> Starting Galaxy</a></li>
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-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
 <ul>
-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>6.8</b> Launching RStudio</a></li>
-<li class="chapter" data-level="6.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>6.9</b> Touring RStudio</a></li>
-<li class="chapter" data-level="6.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>6.10</b> Pausing RStudio</a></li>
-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
 </ul></li>
 <li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="7" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>7</b> Instructor Guide</a></li>
-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
 <ul>
-<li class="chapter" data-level="8.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>8.2.1</b> With no variables set:</a></li>
-<li class="chapter" data-level="8.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>8.2.2</b> With variables set:</a></li>
+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>8.3</b> Student instructions for launching Jupyter</a>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
 <ul>
-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
-<li class="chapter" data-level="8.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>8.3.2</b> Using custom Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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-the-authors.html b/docs/about-the-authors.html
index 61b4548..5d345e5 100644
--- a/docs/about-the-authors.html
+++ b/docs/about-the-authors.html
@@ -123,81 +123,85 @@
 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
-<li class="chapter" data-level="2.2" data-path="research-team.html"><a href="research-team.html#funding"><i class="fa fa-check"></i><b>2.2</b> Funding</a></li>
-<li class="chapter" data-level="2.3" data-path="research-team.html"><a href="research-team.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>2.3</b> Analytical and Computational Support</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
+<li class="chapter" data-level="3" data-path="support.html"><a href="support.html"><i class="fa fa-check"></i><b>3</b> Support</a>
 <ul>
-<li class="chapter" data-level="3.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>3.1</b> Sample Metadata</a></li>
-<li class="chapter" data-level="3.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>3.2</b> Soil Testing Data</a></li>
-<li class="chapter" data-level="3.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>3.3</b> Genomics and Metagenomics Data</a></li>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
 </ul></li>
 <li class="part"><span><b>Using AnVIL</b></span></li>
-<li class="chapter" data-level="4" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>4</b> Billing</a>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
 <ul>
-<li class="chapter" data-level="4.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>4.1</b> Create Google Billing Account</a></li>
-<li class="chapter" data-level="4.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>4.2</b> Add Terra to Google Billing Account</a></li>
-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
-<li class="chapter" data-level="4.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>4.4</b> Set Alerts for Google Billing</a></li>
-<li class="chapter" data-level="4.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>4.5</b> View Spend for Google Billing</a></li>
-<li class="chapter" data-level="4.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>4.6</b> Create Terra Billing Project</a></li>
-<li class="chapter" data-level="4.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>4.7</b> Add Member to Terra Billing Project</a></li>
-<li class="chapter" data-level="4.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>4.8</b> Disable Terra Billing Project</a></li>
+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
 </ul></li>
-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>6.4</b> Starting Galaxy</a></li>
-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
 <ul>
-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>6.8</b> Launching RStudio</a></li>
-<li class="chapter" data-level="6.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>6.9</b> Touring RStudio</a></li>
-<li class="chapter" data-level="6.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>6.10</b> Pausing RStudio</a></li>
-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
 </ul></li>
 <li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="7" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>7</b> Instructor Guide</a></li>
-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
 <ul>
-<li class="chapter" data-level="8.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>8.2.1</b> With no variables set:</a></li>
-<li class="chapter" data-level="8.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>8.2.2</b> With variables set:</a></li>
+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>8.3</b> Student instructions for launching Jupyter</a>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
 <ul>
-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
-<li class="chapter" data-level="8.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>8.3.2</b> Using custom Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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/anvil-workspace.html b/docs/anvil-workspace.html
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   <meta charset="utf-8" />
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
-  <title>Chapter 5 AnVIL Workspace | GDSCN Book: BioDIGS in the Classroom</title>
+  <title>Chapter 6 AnVIL Workspace | GDSCN Book: BioDIGS in the Classroom</title>
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-  <meta property="og:title" content="Chapter 5 AnVIL Workspace | GDSCN Book: BioDIGS in the Classroom" />
+  <meta property="og:title" content="Chapter 6 AnVIL Workspace | GDSCN Book: BioDIGS in the Classroom" />
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-  <meta name="twitter:title" content="Chapter 5 AnVIL Workspace | GDSCN Book: BioDIGS in the Classroom" />
+  <meta name="twitter:title" content="Chapter 6 AnVIL Workspace | GDSCN Book: BioDIGS in the Classroom" />
   
   <meta name="twitter:description" content="This is a companion training guide for BioDIGS, a GDSCN project." />
   
@@ -123,81 +123,85 @@
 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
-<li class="chapter" data-level="2.2" data-path="research-team.html"><a href="research-team.html#funding"><i class="fa fa-check"></i><b>2.2</b> Funding</a></li>
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 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
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 <ul>
-<li class="chapter" data-level="3.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>3.1</b> Sample Metadata</a></li>
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-<li class="chapter" data-level="3.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>3.3</b> Genomics and Metagenomics Data</a></li>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
 </ul></li>
 <li class="part"><span><b>Using AnVIL</b></span></li>
-<li class="chapter" data-level="4" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>4</b> Billing</a>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
 <ul>
-<li class="chapter" data-level="4.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>4.1</b> Create Google Billing Account</a></li>
-<li class="chapter" data-level="4.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>4.2</b> Add Terra to Google Billing Account</a></li>
-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
-<li class="chapter" data-level="4.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>4.4</b> Set Alerts for Google Billing</a></li>
-<li class="chapter" data-level="4.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>4.5</b> View Spend for Google Billing</a></li>
-<li class="chapter" data-level="4.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>4.6</b> Create Terra Billing Project</a></li>
-<li class="chapter" data-level="4.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>4.7</b> Add Member to Terra Billing Project</a></li>
-<li class="chapter" data-level="4.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>4.8</b> Disable Terra Billing Project</a></li>
+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
 </ul></li>
-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>6.4</b> Starting Galaxy</a></li>
-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
 <ul>
-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>6.8</b> Launching RStudio</a></li>
-<li class="chapter" data-level="6.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>6.9</b> Touring RStudio</a></li>
-<li class="chapter" data-level="6.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>6.10</b> Pausing RStudio</a></li>
-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
 </ul></li>
 <li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="7" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>7</b> Instructor Guide</a></li>
-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
 <ul>
-<li class="chapter" data-level="8.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>8.2.1</b> With no variables set:</a></li>
-<li class="chapter" data-level="8.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>8.2.2</b> With variables set:</a></li>
+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>8.3</b> Student instructions for launching Jupyter</a>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
 <ul>
-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
-<li class="chapter" data-level="8.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>8.3.2</b> Using custom Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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>
@@ -233,16 +237,16 @@ <h1>
 <div class="hero-image-container">
   <img class= "hero-image" src="assets/GDSCN_style/dasl_thin_main_image.png">
 </div>
-<div id="anvil-workspace" class="section level1" number="5">
-<h1><span class="header-section-number">Chapter 5</span> AnVIL Workspace</h1>
+<div id="anvil-workspace" class="section level1" number="6">
+<h1><span class="header-section-number">Chapter 6</span> AnVIL Workspace</h1>
 <p>You can easily access the data on AnVIL by cloning the dedicated workspace. These sections guide you through creating an AnVIL account and accessing the workspace.</p>
-<div id="create-google-account" class="section level2" number="5.1">
-<h2><span class="header-section-number">5.1</span> Create Google Account</h2>
+<div id="create-google-account" class="section level2" number="6.1">
+<h2><span class="header-section-number">6.1</span> Create Google Account</h2>
 <p>If you do not already have a Google account that you would like to use for accessing Terra, <a href="https://accounts.google.com/SignUp">create one now</a>.</p>
 <p>If you would like to create a Google account that is associated with your non-Gmail, institutional email address, follow <a href="https://support.terra.bio/hc/en-us/articles/360029186611">these instructions</a>.</p>
 </div>
-<div id="clone-the-workspace" class="section level2" number="5.2">
-<h2><span class="header-section-number">5.2</span> Clone the Workspace</h2>
+<div id="clone-the-workspace" class="section level2" number="6.2">
+<h2><span class="header-section-number">6.2</span> Clone the Workspace</h2>
 <ol style="list-style-type: decimal">
 <li><p><a href="https://anvil.terra.bio/#workspaces">Launch Terra</a></p></li>
 <li><p>Locate the Workspace you want to clone. If a Workspace has been shared with you ahead of time, it will appear in “MY WORKSPACES”. You can clone a Workspace that was shared with you to perform your own analyses. In the screenshot below, no Workspaces have been shared.</p>
diff --git a/docs/background.html b/docs/background.html
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+++ b/docs/background.html
@@ -123,81 +123,85 @@
 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
-<li class="chapter" data-level="2.2" data-path="research-team.html"><a href="research-team.html#funding"><i class="fa fa-check"></i><b>2.2</b> Funding</a></li>
-<li class="chapter" data-level="2.3" data-path="research-team.html"><a href="research-team.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>2.3</b> Analytical and Computational Support</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
+<li class="chapter" data-level="3" data-path="support.html"><a href="support.html"><i class="fa fa-check"></i><b>3</b> Support</a>
 <ul>
-<li class="chapter" data-level="3.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>3.1</b> Sample Metadata</a></li>
-<li class="chapter" data-level="3.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>3.2</b> Soil Testing Data</a></li>
-<li class="chapter" data-level="3.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>3.3</b> Genomics and Metagenomics Data</a></li>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
 </ul></li>
 <li class="part"><span><b>Using AnVIL</b></span></li>
-<li class="chapter" data-level="4" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>4</b> Billing</a>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
 <ul>
-<li class="chapter" data-level="4.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>4.1</b> Create Google Billing Account</a></li>
-<li class="chapter" data-level="4.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>4.2</b> Add Terra to Google Billing Account</a></li>
-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
-<li class="chapter" data-level="4.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>4.4</b> Set Alerts for Google Billing</a></li>
-<li class="chapter" data-level="4.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>4.5</b> View Spend for Google Billing</a></li>
-<li class="chapter" data-level="4.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>4.6</b> Create Terra Billing Project</a></li>
-<li class="chapter" data-level="4.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>4.7</b> Add Member to Terra Billing Project</a></li>
-<li class="chapter" data-level="4.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>4.8</b> Disable Terra Billing Project</a></li>
+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
 </ul></li>
-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>6.4</b> Starting Galaxy</a></li>
-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
 <ul>
-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>6.8</b> Launching RStudio</a></li>
-<li class="chapter" data-level="6.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>6.9</b> Touring RStudio</a></li>
-<li class="chapter" data-level="6.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>6.10</b> Pausing RStudio</a></li>
-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
 </ul></li>
 <li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="7" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>7</b> Instructor Guide</a></li>
-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
 <ul>
-<li class="chapter" data-level="8.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>8.2.1</b> With no variables set:</a></li>
-<li class="chapter" data-level="8.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>8.2.2</b> With variables set:</a></li>
+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>8.3</b> Student instructions for launching Jupyter</a>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
 <ul>
-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
-<li class="chapter" data-level="8.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>8.3.2</b> Using custom Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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/billing.html b/docs/billing.html
index 9a1bb81..fa1297c 100644
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-  <title>Chapter 4 Billing | GDSCN Book: BioDIGS in the Classroom</title>
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-  <meta property="og:title" content="Chapter 4 Billing | GDSCN Book: BioDIGS in the Classroom" />
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-  <meta name="twitter:title" content="Chapter 4 Billing | GDSCN Book: BioDIGS in the Classroom" />
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@@ -123,81 +123,85 @@
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 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
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+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
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+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
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+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
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+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
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-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
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-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
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-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
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-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
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-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
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-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
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+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
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 <li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="7" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>7</b> Instructor Guide</a></li>
-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
 <ul>
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+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>8.3</b> Student instructions for launching Jupyter</a>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
 <ul>
-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
-<li class="chapter" data-level="8.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>8.3.2</b> Using custom Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
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-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
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+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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>
@@ -233,12 +237,12 @@ <h1>
 <div class="hero-image-container">
   <img class= "hero-image" src="assets/GDSCN_style/dasl_thin_main_image.png">
 </div>
-<div id="billing" class="section level1" number="4">
-<h1><span class="header-section-number">Chapter 4</span> Billing</h1>
+<div id="billing" class="section level1" number="5">
+<h1><span class="header-section-number">Chapter 5</span> Billing</h1>
 <p>In order to use AnVIL, you will need to set up a billing account and add members to it. These sections guide you through that process.</p>
 <p><br></p>
-<div id="create-google-billing-account" class="section level2" number="4.1">
-<h2><span class="header-section-number">4.1</span> Create Google Billing Account</h2>
+<div id="create-google-billing-account" class="section level2" number="5.1">
+<h2><span class="header-section-number">5.1</span> Create Google Billing Account</h2>
 <div class="borrowed_chunk">
 <ol style="list-style-type: decimal">
 <li><p>Log in to the <a href="https://console.cloud.google.com/">Google Cloud Platform</a> console using your Google ID. <strong>Make sure to use the same Google account ID you use to log into Terra.</strong></p></li>
@@ -255,8 +259,8 @@ <h2><span class="header-section-number">4.1</span> Create Google Billing Account
 <p>At any point, you can create additional Billing Accounts using the <strong>Create Account</strong> button. We generally recommend creating a new Billing Account for each funding source.</p>
 </div>
 </div>
-<div id="add-terra-to-google-billing-account" class="section level2" number="4.2">
-<h2><span class="header-section-number">4.2</span> Add Terra to Google Billing Account</h2>
+<div id="add-terra-to-google-billing-account" class="section level2" number="5.2">
+<h2><span class="header-section-number">5.2</span> Add Terra to Google Billing Account</h2>
 <div class="borrowed_chunk">
 <p>This gives Terra permission to create projects and send charges to the Google Billing Account, and must be done by an administrator of the Google Billing Account.</p>
 <p>Terra needs to be added as a “Billing Account User”:</p>
@@ -275,8 +279,8 @@ <h2><span class="header-section-number">4.2</span> Add Terra to Google Billing A
 </ol>
 </div>
 </div>
-<div id="add-members-to-google-billing-account" class="section level2" number="4.3">
-<h2><span class="header-section-number">4.3</span> Add Members to Google Billing Account</h2>
+<div id="add-members-to-google-billing-account" class="section level2" number="5.3">
+<h2><span class="header-section-number">5.3</span> Add Members to Google Billing Account</h2>
 <div class="borrowed_chunk">
 <p>Anyone you wish to add to the Billing Account will need their own Google ID.</p>
 <p>To add a member to a Billing Project:</p>
@@ -295,8 +299,8 @@ <h2><span class="header-section-number">4.3</span> Add Members to Google Billing
 </ol>
 </div>
 </div>
-<div id="set-alerts-for-google-billing" class="section level2" number="4.4">
-<h2><span class="header-section-number">4.4</span> Set Alerts for Google Billing</h2>
+<div id="set-alerts-for-google-billing" class="section level2" number="5.4">
+<h2><span class="header-section-number">5.4</span> Set Alerts for Google Billing</h2>
 <div class="borrowed_chunk">
 <ol style="list-style-type: decimal">
 <li><p>Log in to the <a href="https://console.cloud.google.com/">Google Cloud Platform</a> console using the Google ID associated with your Google Cloud projects.</p></li>
@@ -323,8 +327,8 @@ <h2><span class="header-section-number">4.4</span> Set Alerts for Google Billing
 </ol>
 </div>
 </div>
-<div id="view-spend-for-google-billing" class="section level2" number="4.5">
-<h2><span class="header-section-number">4.5</span> View Spend for Google Billing</h2>
+<div id="view-spend-for-google-billing" class="section level2" number="5.5">
+<h2><span class="header-section-number">5.5</span> View Spend for Google Billing</h2>
 <div class="borrowed_chunk">
 <p>You can always check your current spend through the Google Billing console, but remember</p>
 <ul>
@@ -351,8 +355,8 @@ <h2><span class="header-section-number">4.5</span> View Spend for Google Billing
 </ol>
 </div>
 </div>
-<div id="create-terra-billing-project" class="section level2" number="4.6">
-<h2><span class="header-section-number">4.6</span> Create Terra Billing Project</h2>
+<div id="create-terra-billing-project" class="section level2" number="5.6">
+<h2><span class="header-section-number">5.6</span> Create Terra Billing Project</h2>
 <div class="borrowed_chunk">
 <ol style="list-style-type: decimal">
 <li><p><a href="https://anvil.terra.bio/#workspaces">Launch Terra</a> and sign in with your Google account. If this is your first time logging in to Terra, you will need to accept the Terms of Service.</p></li>
@@ -378,8 +382,8 @@ <h2><span class="header-section-number">4.6</span> Create Terra Billing Project<
 <p>The page doesn’t always update as soon as the Billing Project is created. If it’s been a couple of minutes and you don’t see a change, try refreshing the page.</p>
 </div>
 </div>
-<div id="add-member-to-terra-billing-project" class="section level2" number="4.7">
-<h2><span class="header-section-number">4.7</span> Add Member to Terra Billing Project</h2>
+<div id="add-member-to-terra-billing-project" class="section level2" number="5.7">
+<h2><span class="header-section-number">5.7</span> Add Member to Terra Billing Project</h2>
 <div class="borrowed_chunk">
 <ol style="list-style-type: decimal">
 <li><p><a href="https://anvil.terra.bio/#workspaces">Launch Terra</a> and sign in with your Google account.</p></li>
@@ -411,8 +415,8 @@ <h2><span class="header-section-number">4.7</span> Add Member to Terra Billing P
 <p><img src="04-billing_modules_files/figure-html/10-YvYQqI2y32ErihJJMbyLAL4nPIkPA2MLk_6Ee7fXw_g1edc2edcaf8_1_62.png" title="Screenshot of a Terra Billing Project member management page.  The teardrop button for one user is highlighted." alt="Screenshot of a Terra Billing Project member management page.  The teardrop button for one user is highlighted." width="100%" /></p>
 </div>
 </div>
-<div id="disable-terra-billing-project" class="section level2" number="4.8">
-<h2><span class="header-section-number">4.8</span> Disable Terra Billing Project</h2>
+<div id="disable-terra-billing-project" class="section level2" number="5.8">
+<h2><span class="header-section-number">5.8</span> Disable Terra Billing Project</h2>
 <p>By default this module includes a warning to make sure people understand they will lose access to their Workspace buckets. You can remove the warning from this module by setting <code>AnVIL_module_settings$warning</code> to <code>FALSE</code> before running <code>cow::borrow_chapter</code>:</p>
 <pre><code>AnVIL_module_settings &lt;- list(
   warning = FALSE
diff --git a/docs/data-1.html b/docs/data-1.html
index 79822a8..c14f2b6 100644
--- a/docs/data-1.html
+++ b/docs/data-1.html
@@ -4,11 +4,11 @@
 
   <meta charset="utf-8" />
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
-  <title>Chapter 3 Data | GDSCN Book: BioDIGS in the Classroom</title>
+  <title>Chapter 4 Data | GDSCN Book: BioDIGS in the Classroom</title>
   <meta name="description" content="This is a companion training guide for BioDIGS, a GDSCN project." />
   <meta name="generator" content="bookdown 0.24 and GitBook 2.6.7" />
 
-  <meta property="og:title" content="Chapter 3 Data | GDSCN Book: BioDIGS in the Classroom" />
+  <meta property="og:title" content="Chapter 4 Data | GDSCN Book: BioDIGS in the Classroom" />
   <meta property="og:type" content="book" />
   
   
@@ -16,7 +16,7 @@
   
 
   <meta name="twitter:card" content="summary" />
-  <meta name="twitter:title" content="Chapter 3 Data | GDSCN Book: BioDIGS in the Classroom" />
+  <meta name="twitter:title" content="Chapter 4 Data | GDSCN Book: BioDIGS in the Classroom" />
   
   <meta name="twitter:description" content="This is a companion training guide for BioDIGS, a GDSCN project." />
   
@@ -30,7 +30,7 @@
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
   
   <link rel="shortcut icon" href="assets/GDSCN_style/gdscn_favicon.ico" type="image/x-icon" />
-<link rel="prev" href="research-team.html"/>
+<link rel="prev" href="support.html"/>
 <link rel="next" href="billing.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>
@@ -123,81 +123,85 @@
 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
-<li class="chapter" data-level="2.2" data-path="research-team.html"><a href="research-team.html#funding"><i class="fa fa-check"></i><b>2.2</b> Funding</a></li>
-<li class="chapter" data-level="2.3" data-path="research-team.html"><a href="research-team.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>2.3</b> Analytical and Computational Support</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
+<li class="chapter" data-level="3" data-path="support.html"><a href="support.html"><i class="fa fa-check"></i><b>3</b> Support</a>
 <ul>
-<li class="chapter" data-level="3.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>3.1</b> Sample Metadata</a></li>
-<li class="chapter" data-level="3.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>3.2</b> Soil Testing Data</a></li>
-<li class="chapter" data-level="3.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>3.3</b> Genomics and Metagenomics Data</a></li>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
 </ul></li>
 <li class="part"><span><b>Using AnVIL</b></span></li>
-<li class="chapter" data-level="4" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>4</b> Billing</a>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
 <ul>
-<li class="chapter" data-level="4.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>4.1</b> Create Google Billing Account</a></li>
-<li class="chapter" data-level="4.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>4.2</b> Add Terra to Google Billing Account</a></li>
-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
-<li class="chapter" data-level="4.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>4.4</b> Set Alerts for Google Billing</a></li>
-<li class="chapter" data-level="4.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>4.5</b> View Spend for Google Billing</a></li>
-<li class="chapter" data-level="4.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>4.6</b> Create Terra Billing Project</a></li>
-<li class="chapter" data-level="4.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>4.7</b> Add Member to Terra Billing Project</a></li>
-<li class="chapter" data-level="4.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>4.8</b> Disable Terra Billing Project</a></li>
+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
 </ul></li>
-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>6.4</b> Starting Galaxy</a></li>
-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
 <ul>
-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>6.8</b> Launching RStudio</a></li>
-<li class="chapter" data-level="6.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>6.9</b> Touring RStudio</a></li>
-<li class="chapter" data-level="6.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>6.10</b> Pausing RStudio</a></li>
-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
 </ul></li>
 <li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="7" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>7</b> Instructor Guide</a></li>
-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
 <ul>
-<li class="chapter" data-level="8.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>8.2.1</b> With no variables set:</a></li>
-<li class="chapter" data-level="8.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>8.2.2</b> With variables set:</a></li>
+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>8.3</b> Student instructions for launching Jupyter</a>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
 <ul>
-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
-<li class="chapter" data-level="8.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>8.3.2</b> Using custom Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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>
@@ -233,21 +237,21 @@ <h1>
 <div class="hero-image-container">
   <img class= "hero-image" src="assets/GDSCN_style/dasl_thin_main_image.png">
 </div>
-<div id="data-1" class="section level1" number="3">
-<h1><span class="header-section-number">Chapter 3</span> Data</h1>
+<div id="data-1" class="section level1" number="4">
+<h1><span class="header-section-number">Chapter 4</span> Data</h1>
 <p>There are currently three major kinds of data available from BioDIGS: sample metadata, soil testing data, and genomics and metagenomics data. All of these are available for use in your classroom.</p>
-<div id="sample-metadata" class="section level2" number="3.1">
-<h2><span class="header-section-number">3.1</span> Sample Metadata</h2>
+<div id="sample-metadata" class="section level2" number="4.1">
+<h2><span class="header-section-number">4.1</span> Sample Metadata</h2>
 <p>This dataset contains information about the samples themselves, including GPS coordinates for the sample location, date the sample was taken, and the site name. This dataset is also available from the <a href="https://biodigs.org/#site_data">BioDIGS website</a></p>
 <p>You can also see images of each sampling site and soil characteristics at the <a href="https://biodigs.org/#sample_map">sample map</a>.</p>
 </div>
-<div id="soil-testing-data" class="section level2" number="3.2">
-<h2><span class="header-section-number">3.2</span> Soil Testing Data</h2>
+<div id="soil-testing-data" class="section level2" number="4.2">
+<h2><span class="header-section-number">4.2</span> Soil Testing Data</h2>
 <p>This dataset includes basic information about the soil itself like pH, percentage of organic matter, variety of soil metal concentrations. The complete data dictionary is available <a href="https://docs.google.com/spreadsheets/d/109xYUM48rjj33B76hZ3bNlrm8u-_S6uyoE_3wSCp0r0/edit#gid=188448677">here</a>. The dataset is available at the <a href="https://biodigs.org/#soil_data">BioDIGS website</a>.</p>
 <p>This dataset was generated by the <a href="https://www.udel.edu/canr/cooperative-extension/environmental-stewardship/soil-testing/">Delaware Soil Testing Program</a> at the University of Delaware.</p>
 </div>
-<div id="genomics-and-metagenomics-data" class="section level2" number="3.3">
-<h2><span class="header-section-number">3.3</span> Genomics and Metagenomics Data</h2>
+<div id="genomics-and-metagenomics-data" class="section level2" number="4.3">
+<h2><span class="header-section-number">4.3</span> Genomics and Metagenomics Data</h2>
 <p>You can access this data in both raw and processed forms.</p>
 <p>The Illumina and Nanopore sequences were generated at the <a href="https://grcf.jhmi.edu/">Johns Hopkins University Genetic Resources Core Facility</a>. PacBio sequencing was done by <a href="https://www.pacb.com/">PacBio</a> directly.</p>
 <p>More information coming soon!</p>
@@ -270,7 +274,7 @@ <h2><span class="header-section-number">3.3</span> Genomics and Metagenomics Dat
           </div>
         </div>
       </div>
-<a href="research-team.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
+<a href="support.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
 <a href="billing.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
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diff --git a/docs/index.html b/docs/index.html
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@@ -123,81 +123,85 @@
 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
-<li class="chapter" data-level="2.2" data-path="research-team.html"><a href="research-team.html#funding"><i class="fa fa-check"></i><b>2.2</b> Funding</a></li>
-<li class="chapter" data-level="2.3" data-path="research-team.html"><a href="research-team.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>2.3</b> Analytical and Computational Support</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
+<li class="chapter" data-level="3" data-path="support.html"><a href="support.html"><i class="fa fa-check"></i><b>3</b> Support</a>
 <ul>
-<li class="chapter" data-level="3.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>3.1</b> Sample Metadata</a></li>
-<li class="chapter" data-level="3.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>3.2</b> Soil Testing Data</a></li>
-<li class="chapter" data-level="3.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>3.3</b> Genomics and Metagenomics Data</a></li>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
 </ul></li>
 <li class="part"><span><b>Using AnVIL</b></span></li>
-<li class="chapter" data-level="4" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>4</b> Billing</a>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
 <ul>
-<li class="chapter" data-level="4.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>4.1</b> Create Google Billing Account</a></li>
-<li class="chapter" data-level="4.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>4.2</b> Add Terra to Google Billing Account</a></li>
-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
-<li class="chapter" data-level="4.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>4.4</b> Set Alerts for Google Billing</a></li>
-<li class="chapter" data-level="4.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>4.5</b> View Spend for Google Billing</a></li>
-<li class="chapter" data-level="4.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>4.6</b> Create Terra Billing Project</a></li>
-<li class="chapter" data-level="4.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>4.7</b> Add Member to Terra Billing Project</a></li>
-<li class="chapter" data-level="4.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>4.8</b> Disable Terra Billing Project</a></li>
+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
 </ul></li>
-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>6.4</b> Starting Galaxy</a></li>
-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
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-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
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-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
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-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
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+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
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+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
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+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
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+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
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+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
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-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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>
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 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
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 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
+<li class="chapter" data-level="3" data-path="support.html"><a href="support.html"><i class="fa fa-check"></i><b>3</b> Support</a>
 <ul>
-<li class="chapter" data-level="3.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>3.1</b> Sample Metadata</a></li>
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-<li class="chapter" data-level="3.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>3.3</b> Genomics and Metagenomics Data</a></li>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
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-<li class="chapter" data-level="4" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>4</b> Billing</a>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
 <ul>
-<li class="chapter" data-level="4.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>4.1</b> Create Google Billing Account</a></li>
-<li class="chapter" data-level="4.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>4.2</b> Add Terra to Google Billing Account</a></li>
-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
-<li class="chapter" data-level="4.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>4.4</b> Set Alerts for Google Billing</a></li>
-<li class="chapter" data-level="4.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>4.5</b> View Spend for Google Billing</a></li>
-<li class="chapter" data-level="4.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>4.6</b> Create Terra Billing Project</a></li>
-<li class="chapter" data-level="4.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>4.7</b> Add Member to Terra Billing Project</a></li>
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+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
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-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
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-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
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-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
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+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
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+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
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-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
 <ul>
-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
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-<li class="chapter" data-level="6.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>6.8</b> Launching RStudio</a></li>
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-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
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-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
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-<li class="chapter" data-level="8.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>8.2.1</b> With no variables set:</a></li>
-<li class="chapter" data-level="8.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>8.2.2</b> With variables set:</a></li>
+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
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-<li class="chapter" data-level="8.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>8.3</b> Student instructions for launching Jupyter</a>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
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-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
-<li class="chapter" data-level="8.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>8.3.2</b> Using custom Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
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-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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>
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-<div id="instructor-guide" class="section level1" number="7">
-<h1><span class="header-section-number">Chapter 7</span> Instructor Guide</h1>
+<div id="instructor-guide" class="section level1" number="8">
+<h1><span class="header-section-number">Chapter 8</span> Instructor Guide</h1>
 </div>
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-  <title>Chapter 6 Programming Platforms | GDSCN Book: BioDIGS in the Classroom</title>
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-  <meta name="twitter:title" content="Chapter 6 Programming Platforms | GDSCN Book: BioDIGS in the Classroom" />
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 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
-<li class="chapter" data-level="2.2" data-path="research-team.html"><a href="research-team.html#funding"><i class="fa fa-check"></i><b>2.2</b> Funding</a></li>
-<li class="chapter" data-level="2.3" data-path="research-team.html"><a href="research-team.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>2.3</b> Analytical and Computational Support</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
+<li class="chapter" data-level="3" data-path="support.html"><a href="support.html"><i class="fa fa-check"></i><b>3</b> Support</a>
 <ul>
-<li class="chapter" data-level="3.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>3.1</b> Sample Metadata</a></li>
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-<li class="chapter" data-level="3.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>3.3</b> Genomics and Metagenomics Data</a></li>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
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 <li class="part"><span><b>Using AnVIL</b></span></li>
-<li class="chapter" data-level="4" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>4</b> Billing</a>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
 <ul>
-<li class="chapter" data-level="4.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>4.1</b> Create Google Billing Account</a></li>
-<li class="chapter" data-level="4.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>4.2</b> Add Terra to Google Billing Account</a></li>
-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
-<li class="chapter" data-level="4.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>4.4</b> Set Alerts for Google Billing</a></li>
-<li class="chapter" data-level="4.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>4.5</b> View Spend for Google Billing</a></li>
-<li class="chapter" data-level="4.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>4.6</b> Create Terra Billing Project</a></li>
-<li class="chapter" data-level="4.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>4.7</b> Add Member to Terra Billing Project</a></li>
-<li class="chapter" data-level="4.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>4.8</b> Disable Terra Billing Project</a></li>
+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
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-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
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-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
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-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>6.4</b> Starting Galaxy</a></li>
-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
 <ul>
-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>6.8</b> Launching RStudio</a></li>
-<li class="chapter" data-level="6.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>6.9</b> Touring RStudio</a></li>
-<li class="chapter" data-level="6.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>6.10</b> Pausing RStudio</a></li>
-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
 </ul></li>
 <li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="7" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>7</b> Instructor Guide</a></li>
-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
 <ul>
-<li class="chapter" data-level="8.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>8.2.1</b> With no variables set:</a></li>
-<li class="chapter" data-level="8.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>8.2.2</b> With variables set:</a></li>
+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>8.3</b> Student instructions for launching Jupyter</a>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
 <ul>
-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
-<li class="chapter" data-level="8.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>8.3.2</b> Using custom Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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>
@@ -233,30 +237,30 @@ <h1>
 <div class="hero-image-container">
   <img class= "hero-image" src="assets/GDSCN_style/dasl_thin_main_image.png">
 </div>
-<div id="programming-platforms" class="section level1" number="6">
-<h1><span class="header-section-number">Chapter 6</span> Programming Platforms</h1>
+<div id="programming-platforms" class="section level1" number="7">
+<h1><span class="header-section-number">Chapter 7</span> Programming Platforms</h1>
 <p>These sections provide a general overview of how to use RStudio and Galaxy on AnVIL.</p>
 <p><br></p>
-<div id="video-overview-on-using-jupyter-notebooks" class="section level2" number="6.1">
-<h2><span class="header-section-number">6.1</span> Video overview on using Jupyter Notebooks</h2>
+<div id="video-overview-on-using-jupyter-notebooks" class="section level2" number="7.1">
+<h2><span class="header-section-number">7.1</span> Video overview on using Jupyter Notebooks</h2>
 <p>Here is a video tutorial that describes the basics of using Jupyter Notebook on AnVIL.</p>
 <iframe src="https://drive.google.com/file/d/1ZhPYFy4zuAHhPhF6T4pUgSReBmPJM-wg/preview" width="640" height="360" allow="autoplay">
 </iframe>
-<div id="objectives" class="section level3" number="6.1.1">
-<h3><span class="header-section-number">6.1.1</span> Objectives</h3>
+<div id="objectives" class="section level3" number="7.1.1">
+<h3><span class="header-section-number">7.1.1</span> Objectives</h3>
 <ul>
 <li>Start compute for your Jupyter environment</li>
 <li>Create notebook to perform analysis</li>
 <li>Stop compute to minimize expenses</li>
 </ul>
 </div>
-<div id="slides" class="section level3" number="6.1.2">
-<h3><span class="header-section-number">6.1.2</span> Slides</h3>
+<div id="slides" class="section level3" number="7.1.2">
+<h3><span class="header-section-number">7.1.2</span> Slides</h3>
 <p>The slides for this tutorial are are located <a href="https://docs.google.com/presentation/d/1GYUP874Qd7K3S0Ls6iWY_M4jywpRb53qw0f78OBCFwk">here</a>.</p>
 </div>
 </div>
-<div id="launching-jupyter" class="section level2" number="6.2">
-<h2><span class="header-section-number">6.2</span> Launching Jupyter</h2>
+<div id="launching-jupyter" class="section level2" number="7.2">
+<h2><span class="header-section-number">7.2</span> Launching Jupyter</h2>
 <div class="borrowed_chunk">
 <div class="warning">
 <p>AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select a cloud computing environment appropriate to your needs to avoid runaway costs. If you are uncertain, start with the default settings; it is fairly easy to increase your compute resources later, if needed, but harder to scale down.</p>
@@ -286,34 +290,34 @@ <h2><span class="header-section-number">6.2</span> Launching Jupyter</h2>
 </ol>
 </div>
 </div>
-<div id="video-overview-on-using-galaxy" class="section level2" number="6.3">
-<h2><span class="header-section-number">6.3</span> Video overview on using Galaxy</h2>
+<div id="video-overview-on-using-galaxy" class="section level2" number="7.3">
+<h2><span class="header-section-number">7.3</span> Video overview on using Galaxy</h2>
 <p>Here is a video tutorial that describes the basics of using Galaxy on AnVIL.</p>
 <iframe src="https://drive.google.com/file/d/16QEY8x-gBsUkKEeO3w_H-I4SLIBPloXd/preview" width="640" height="360" allow="autoplay">
 </iframe>
-<div id="objectives-1" class="section level3" number="6.3.1">
-<h3><span class="header-section-number">6.3.1</span> Objectives</h3>
+<div id="objectives-1" class="section level3" number="7.3.1">
+<h3><span class="header-section-number">7.3.1</span> Objectives</h3>
 <ul>
 <li>Start compute for your Galaxy on AnVIL</li>
 <li>Run tool to quality control sequencing reads</li>
 <li>Stop compute to minimize expenses</li>
 </ul>
 </div>
-<div id="slides-1" class="section level3" number="6.3.2">
-<h3><span class="header-section-number">6.3.2</span> Slides</h3>
+<div id="slides-1" class="section level3" number="7.3.2">
+<h3><span class="header-section-number">7.3.2</span> Slides</h3>
 <p>The slides for this tutorial are are located <a href="https://docs.google.com/presentation/d/1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q">here</a>.</p>
 </div>
 </div>
-<div id="starting-galaxy" class="section level2" number="6.4">
-<h2><span class="header-section-number">6.4</span> Starting Galaxy</h2>
+<div id="starting-galaxy" class="section level2" number="7.4">
+<h2><span class="header-section-number">7.4</span> Starting Galaxy</h2>
 <div class="borrowed_chunk">
 <p>Note that, in order to use Galaxy, you must have access to a Terra Workspace with permission to compute (i.e. you must be a “Writer” or “Owner” of the Workspace).</p>
 <p>Open your Workspace, and click on the “NOTEBOOKS” tab. Next, click on “Create a Cloud Environment for Galaxy”. You should see a popup window on the right side of the screen. Click on “NEXT” and “CREATE” to keep all settings as-is. This will take 8-10 minutes. When it is done, click “LAUNCH GALAXY”.</p>
 <p><img src="06-using_platforms_modules_files/figure-html/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_ged15532ded_0_788.png" title="Screenshot of the Workspace Notebooks tab. The notebook tab name and the plus button that starts a cloud environment for Galaxy have been highlighted," alt="Screenshot of the Workspace Notebooks tab. The notebook tab name and the plus button that starts a cloud environment for Galaxy have been highlighted," width="100%" /></p>
 </div>
 </div>
-<div id="navigating-galaxy" class="section level2" number="6.5">
-<h2><span class="header-section-number">6.5</span> Navigating Galaxy</h2>
+<div id="navigating-galaxy" class="section level2" number="7.5">
+<h2><span class="header-section-number">7.5</span> Navigating Galaxy</h2>
 <div class="borrowed_chunk">
 <p>Notice the three main sections.</p>
 <p><strong>Tools</strong> - These are all of the bioinformatics tool packages available for you to use.</p>
@@ -323,8 +327,8 @@ <h2><span class="header-section-number">6.5</span> Navigating Galaxy</h2>
 <p>On the welcome page, there are links to tutorials. You may try these out on your own. If you want to try a new analysis this is a good place to start.</p>
 </div>
 </div>
-<div id="deleting-galaxy" class="section level2" number="6.6">
-<h2><span class="header-section-number">6.6</span> Deleting Galaxy</h2>
+<div id="deleting-galaxy" class="section level2" number="7.6">
+<h2><span class="header-section-number">7.6</span> Deleting Galaxy</h2>
 <div class="borrowed_chunk">
 <p>Once you are done with your activity, you’ll need to shut down your Galaxy cloud environment. This frees up the cloud resources for others and minimizes computing cost. The following steps will delete your work, so make sure you are completely finished at this point. Otherwise, you will have to repeat your work from the previous steps.</p>
 <p>Return to AnVIL, and find the Galaxy logo that shows your cloud environment is running. Click on this logo:</p>
@@ -335,26 +339,26 @@ <h2><span class="header-section-number">6.6</span> Deleting Galaxy</h2>
 <p><img src="06-using_platforms_modules_files/figure-html/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_gf243efded1_0_146.png" title="Screenshot of the cloud environment pop out menu. The “Delete everything, including persistent disk” radio button has been checked and is highlighted. The “DELETE” button is highlighted." alt="Screenshot of the cloud environment pop out menu. The “Delete everything, including persistent disk” radio button has been checked and is highlighted. The “DELETE” button is highlighted." width="100%" /></p>
 </div>
 </div>
-<div id="video-overview-on-using-rstudio" class="section level2" number="6.7">
-<h2><span class="header-section-number">6.7</span> Video overview on using RStudio</h2>
+<div id="video-overview-on-using-rstudio" class="section level2" number="7.7">
+<h2><span class="header-section-number">7.7</span> Video overview on using RStudio</h2>
 <p>Here is a video tutorial that describes the basics of using RStudio on AnVIL.</p>
 <iframe src="https://drive.google.com/file/d/1v72ZG8JIRDUaewFQgGfcCO_qoM4eYmYX/preview" width="640" height="360" allow="autoplay">
 </iframe>
-<div id="objectives-2" class="section level3" number="6.7.1">
-<h3><span class="header-section-number">6.7.1</span> Objectives</h3>
+<div id="objectives-2" class="section level3" number="7.7.1">
+<h3><span class="header-section-number">7.7.1</span> Objectives</h3>
 <ul>
 <li>Start compute for your RStudio environment</li>
 <li>Tour RStudio on AnVIL</li>
 <li>Stop compute to minimize expenses</li>
 </ul>
 </div>
-<div id="slides-2" class="section level3" number="6.7.2">
-<h3><span class="header-section-number">6.7.2</span> Slides</h3>
+<div id="slides-2" class="section level3" number="7.7.2">
+<h3><span class="header-section-number">7.7.2</span> Slides</h3>
 <p>The slides for this tutorial are are located <a href="https://docs.google.com/presentation/d/1eypYLLqD11-NwHLs4adGpcuSB07dYEJfAaALSMvgzqw">here</a>.</p>
 </div>
 </div>
-<div id="launching-rstudio" class="section level2" number="6.8">
-<h2><span class="header-section-number">6.8</span> Launching RStudio</h2>
+<div id="launching-rstudio" class="section level2" number="7.8">
+<h2><span class="header-section-number">7.8</span> Launching RStudio</h2>
 <div class="borrowed_chunk">
 <div class="warning">
 <p>AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select a cloud computing environment appropriate to your needs to avoid runaway costs. If you are uncertain, start with the default settings; it is fairly easy to increase your compute resources later, if needed, but harder to scale down.</p>
@@ -386,8 +390,8 @@ <h2><span class="header-section-number">6.8</span> Launching RStudio</h2>
 </ol>
 </div>
 </div>
-<div id="touring-rstudio" class="section level2" number="6.9">
-<h2><span class="header-section-number">6.9</span> Touring RStudio</h2>
+<div id="touring-rstudio" class="section level2" number="7.9">
+<h2><span class="header-section-number">7.9</span> Touring RStudio</h2>
 <div class="borrowed_chunk">
 <p>Next, we will be using RStudio and the package <code>Glimma</code> to create interactive plots. See <a href="https://bioconductor.org/packages/release/bioc/vignettes/Glimma/inst/doc/limma_edger.html">this vignette</a> for more information.</p>
 <ol style="list-style-type: decimal">
@@ -417,8 +421,8 @@ <h2><span class="header-section-number">6.9</span> Touring RStudio</h2>
 </ol>
 </div>
 </div>
-<div id="pausing-rstudio" class="section level2" number="6.10">
-<h2><span class="header-section-number">6.10</span> Pausing RStudio</h2>
+<div id="pausing-rstudio" class="section level2" number="7.10">
+<h2><span class="header-section-number">7.10</span> Pausing RStudio</h2>
 <div class="borrowed_chunk">
 <ol style="list-style-type: decimal">
 <li><p>The right-hand side icon reminds you that you are accruing cloud computing costs. If you don’t see this icon, you may need to scroll to the right.</p>
@@ -431,8 +435,8 @@ <h2><span class="header-section-number">6.10</span> Pausing RStudio</h2>
 </div>
 </div>
 </div>
-<div id="deleting-rstudio" class="section level2" number="6.11">
-<h2><span class="header-section-number">6.11</span> Deleting RStudio</h2>
+<div id="deleting-rstudio" class="section level2" number="7.11">
+<h2><span class="header-section-number">7.11</span> Deleting RStudio</h2>
 <div class="borrowed_chunk">
 <ol style="list-style-type: decimal">
 <li><p>Pausing your cloud environment only temporarily stops your work. When you are ready to delete the cloud environment, click on the RStudio icon on the right-hand side and select “Settings”. If you don’t see this icon, you may need to scroll to the right.</p>
diff --git a/docs/reference-keys.txt b/docs/reference-keys.txt
index 020ae5c..2826e8a 100644
--- a/docs/reference-keys.txt
+++ b/docs/reference-keys.txt
@@ -9,7 +9,9 @@ why-soil-microbes
 heavy-metals-and-human-health
 research-team
 soil-sampling
+support
 funding
+sponsors
 analytical-and-computational-support
 data-1
 sample-metadata
diff --git a/docs/references.html b/docs/references.html
index 278349c..a66efea 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 9 References | GDSCN Book: BioDIGS in the Classroom</title>
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-  <meta name="twitter:title" content="Chapter 9 References | GDSCN Book: BioDIGS in the Classroom" />
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@@ -123,81 +123,85 @@
 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
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 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
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 <ul>
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+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
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+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
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+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
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-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
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+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
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-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
 </ul></li>
-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>6.4</b> Starting Galaxy</a></li>
-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
 <ul>
-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>6.8</b> Launching RStudio</a></li>
-<li class="chapter" data-level="6.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>6.9</b> Touring RStudio</a></li>
-<li class="chapter" data-level="6.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>6.10</b> Pausing RStudio</a></li>
-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
 </ul></li>
 <li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="7" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>7</b> Instructor Guide</a></li>
-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
 <ul>
-<li class="chapter" data-level="8.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>8.2.1</b> With no variables set:</a></li>
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+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
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+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
 <ul>
-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
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+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
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-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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>
@@ -233,8 +237,8 @@ <h1>
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-<div id="references" class="section level1" number="9">
-<h1><span class="header-section-number">Chapter 9</span> References</h1>
+<div id="references" class="section level1" number="10">
+<h1><span class="header-section-number">Chapter 10</span> References</h1>
 
 <div id="refs" class="references csl-bib-body hanging-indent">
 <div id="ref-BrevikBurgess2014" class="csl-entry">
diff --git a/docs/research-team.html b/docs/research-team.html
index f213716..6488411 100644
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+++ b/docs/research-team.html
@@ -31,7 +31,7 @@
   
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@@ -123,81 +123,85 @@
 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
-<li class="chapter" data-level="2.2" data-path="research-team.html"><a href="research-team.html#funding"><i class="fa fa-check"></i><b>2.2</b> Funding</a></li>
-<li class="chapter" data-level="2.3" data-path="research-team.html"><a href="research-team.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>2.3</b> Analytical and Computational Support</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
+<li class="chapter" data-level="3" data-path="support.html"><a href="support.html"><i class="fa fa-check"></i><b>3</b> Support</a>
 <ul>
-<li class="chapter" data-level="3.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>3.1</b> Sample Metadata</a></li>
-<li class="chapter" data-level="3.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>3.2</b> Soil Testing Data</a></li>
-<li class="chapter" data-level="3.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>3.3</b> Genomics and Metagenomics Data</a></li>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
 </ul></li>
 <li class="part"><span><b>Using AnVIL</b></span></li>
-<li class="chapter" data-level="4" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>4</b> Billing</a>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
 <ul>
-<li class="chapter" data-level="4.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>4.1</b> Create Google Billing Account</a></li>
-<li class="chapter" data-level="4.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>4.2</b> Add Terra to Google Billing Account</a></li>
-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
-<li class="chapter" data-level="4.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>4.4</b> Set Alerts for Google Billing</a></li>
-<li class="chapter" data-level="4.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>4.5</b> View Spend for Google Billing</a></li>
-<li class="chapter" data-level="4.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>4.6</b> Create Terra Billing Project</a></li>
-<li class="chapter" data-level="4.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>4.7</b> Add Member to Terra Billing Project</a></li>
-<li class="chapter" data-level="4.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>4.8</b> Disable Terra Billing Project</a></li>
+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
 </ul></li>
-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>6.4</b> Starting Galaxy</a></li>
-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
 <ul>
-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>6.8</b> Launching RStudio</a></li>
-<li class="chapter" data-level="6.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>6.9</b> Touring RStudio</a></li>
-<li class="chapter" data-level="6.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>6.10</b> Pausing RStudio</a></li>
-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
 </ul></li>
 <li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="7" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>7</b> Instructor Guide</a></li>
-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
 <ul>
-<li class="chapter" data-level="8.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>8.2.1</b> With no variables set:</a></li>
-<li class="chapter" data-level="8.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>8.2.2</b> With variables set:</a></li>
+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>8.3</b> Student instructions for launching Jupyter</a>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
 <ul>
-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
-<li class="chapter" data-level="8.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>8.3.2</b> Using custom Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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>
@@ -260,16 +264,6 @@ <h2><span class="header-section-number">2.1</span> Soil sampling</h2>
 <li><strong>Seattle, WA</strong>: North Seattle College, Pierce College</li>
 <li><strong>Tsaile, AZ</strong>: Diné College</li>
 </ul>
-</div>
-<div id="funding" class="section level2" number="2.2">
-<h2><span class="header-section-number">2.2</span> Funding</h2>
-<p>Funding for this project has been provided by the <a href="https://www.genome.gov/">National Human Genome Research Institute</a> (Contract # 75N92022P00232 awarded to Johns Hopkins University), as well as by donations from <a href="https://www.pacb.com/">PacBio</a> and <a href="https://www.cosmosid.com/">CosmosID</a>.</p>
-<p><a href="https://www.agbt.org/">Advances in Genome Biology and Technology</a> provided funding support for several team members to attend AGBT 2024.</p>
-</div>
-<div id="analytical-and-computational-support" class="section level2" number="2.3">
-<h2><span class="header-section-number">2.3</span> Analytical and Computational Support</h2>
-<p>Computational support has been provided by NHGRI’s <a href="https://anvilproject.org/">AnVIL</a> cloud computing platform and <a href="usegalaxy.org">Galaxy</a>.</p>
-
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-[["index.html", "GDSCN Book: BioDIGS in the Classroom About this Book 0.1 Target Audience 0.2 Platform 0.3 Data", " GDSCN Book: BioDIGS in the Classroom February 02, 2024 About this Book This is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. Visit the BioDIGS (BioDiversity and Informatics for Genomics Scholars) website here for more information about this collaborative, distributed research project, including how you can get involved! The GDSCN (Genomics Data Science Community Network) is a consortium of educators who aim to create a world where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. You can find more information about its mission and initiatives here. BioDIGS logo 0.1 Target Audience The activities in this guide are written for undergraduate students and beginning graduate students. Some sections require basic understanding of the R programming language, which is indicated at the beginning of the chapter. 0.2 Platform The activities in this guide are demonstrated on NHGRI’s AnVIL cloud computing platform. AnVIL is the preferred computing platform for the GDSCN. However, all of these activities can be done using your personal installation of R or using the online Galaxy portal. 0.3 Data The data generated by the BioDIGS project is available through the BioDIGS website, as well as through an AnVIL workspace. Data about the soil itself as well as soil metal content was generated by the Delaware Soil Testing Program at the University of Delaware. Sequences were generated by the Johns Hopkins University Genetic Resources Core Facility and by PacBio. "],["background.html", "Chapter 1 Background 1.1 What is genomics? 1.2 What is data science? 1.3 What is cloud computing? 1.4 Why soil microbes? 1.5 Heavy metals and human health", " Chapter 1 Background One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student’s interest in pursuing STEM careers (Russell, Hancock, and McCullough 2007). It can also lead to improved scientific reasoning and increased academic performance overall (Buffalari et al. 2020). However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science (Canner et al. 2017; GDSCN 2022). The BioDIGS Project aims to be at the intersection of genomics, data science, cloud computing, and education. 1.1 What is genomics? Genomics broadly refers to the study of genomes, which are an organism’s complete set of DNA. This includes both genes and non-coding regions of DNA. Traditional genomics involves sequencing and analyzing the genome of individual species. Metagenomics expands genomics to look at the collective genomes of entire communities of organisms in an environmental sample, like soil. It allows researchers to study not just the genes of culturable or isolated organisms, but the entirety of genetic material present in a given environment. By using genomic techniques to survey the soil microbes, we can identify everything in the soil, including microbes that no one has identified before. We are doing both traditional genomics and metagenomics as part of BioDIGS. 1.2 What is data science? Data science is an interdisciplinary field that uses scientific methods, processes, algorithms and systems to extract knowledge and insights from structured and unstructured data. It includes collecting, cleaning, and combining data from multiple databases, exploring data and developing statistical and machine learning models to identify patterns in complex datasets, and creating tools to efficiently store, process, and access large amounts of data. 1.3 What is cloud computing? Cloud computing just means using the internet to get access to powerful computer resources like storage, servers, databases, networking tools, and specialized software programs. Instead of having to buy and maintain their own powerful computers, storage servers, and other systems, users can pay to use them through an internet connection as needed. Users only pay for what they need, when they actually use it, and professionals update and maintain the systems in large data centers. It is a particularly useful tool for researchers and students at smaller institutions with limited computational services, especially when working with complex databases. The genome assembly and analyses for BioDIGS have been done using the NHGRI AnVIL cloud computing platform, as well as Galaxy. 1.4 Why soil microbes? It can be challenging to include undergraduates in human genomic and health research, especially in a classroom context. Both human genetic data and human health data are protected data, which limits the sort of information students can access without undergoing specialized ethics training. However, the same sorts of data cleaning and analysis methods used for human genomic data are also used for microbial genomic data, which does not have the same sort of legal protections as human genetic data. This makes it ideal for training undergraduate students at the beginning of their careers and can be used to prepare students for future research in human genomics and health (Jurkowski, Reid, and Labov 2017). Additionally, the microbes in the soil can have big impacts on our health (Brevik and Burgess 2014). 1.5 Heavy metals and human health Human activities that change the landscape can also change what sorts of inorganic and abiotic compounds we find in the soil, particularly increasing the amount of heavy metals (Yan et al. 2020). When cars drive on roads, compounds from the exhaust, oil, and other fluids might settle onto the roads and be washed into the soil. When we put salt on roads, parking lots, and sidewalks, the salts themselves will eventually be washed away and enter the ecosystem through both water and soil. Chemicals from factories and other businesses also leech into our environment. Previous research has demonstrated that in areas with more human activity, like cities, soils include greater concentrations of heavy metals than found in rural areas with limited human populations (Khan et al. 2023; Wang, Birch, and Liu 2022). Increased heavy metal concentrations also disproportionately affect lower-income and predominantly minority areas (Jones et al. 2022). Research suggests that increased heavy metal concentration in soils has major impacts on the soil microbial community. In particular, increased heavy metal concentration is associated with an increase in soil bacteria that have antibiotic resistance markers (Gorovtsov, Sazykin, and Sazykina 2018; Nguyen et al. 2019; Sun, Xu, and Fan 2021). "],["research-team.html", "Chapter 2 Research Team 2.1 Soil sampling 2.2 Funding 2.3 Analytical and Computational Support", " Chapter 2 Research Team This project is coordinated by the Genomics Data Science Community Network (GDSCN). You can read more about the GDSCN and its mission at the network website. 2.1 Soil sampling This map shows the current sampling locations for the BioDIGS project. The extensive network of the GDSCN has made this data collection possible. Soil sampling for this project was done by both faculty and student volunteers from schools that aren’t traditional R1 research institutions. Many of the faculty are also members of the GDSCN. This list of locations reflects GDSCN institutions and friends of GDSCN who have collected soil samples. Annandale, VA: Northern Virginia Community College Atlanta, GA: Spelman College Baltimore, MD: College of Southern Maryland, Notre Dame College of Maryland, Towson University Bismark, ND: United Tribes Technical College El Paso, TX: El Paso Community College, The University of Texas at El Paso Fresno, CA: Clovis Community College Greensboro, NC: North Carolina A&amp;T State University Harrisonburg, VA: James Madison University Honolulu, Hawai’i: University of Hawai’i at Mānoa Las Cruces, NM: Doña Ana Community College Montgomery County, MD: Montgomery College, Towson University Nashville, TN: Meharry Medical College New York, NY: Guttman Community College CUNY Petersburg, VA: Virginia State University Seattle, WA: North Seattle College, Pierce College Tsaile, AZ: Diné College 2.2 Funding Funding for this project has been provided by the National Human Genome Research Institute (Contract # 75N92022P00232 awarded to Johns Hopkins University), as well as by donations from PacBio and CosmosID. Advances in Genome Biology and Technology provided funding support for several team members to attend AGBT 2024. 2.3 Analytical and Computational Support Computational support has been provided by NHGRI’s AnVIL cloud computing platform and Galaxy. "],["data-1.html", "Chapter 3 Data 3.1 Sample Metadata 3.2 Soil Testing Data 3.3 Genomics and Metagenomics Data", " Chapter 3 Data There are currently three major kinds of data available from BioDIGS: sample metadata, soil testing data, and genomics and metagenomics data. All of these are available for use in your classroom. 3.1 Sample Metadata This dataset contains information about the samples themselves, including GPS coordinates for the sample location, date the sample was taken, and the site name. This dataset is also available from the BioDIGS website You can also see images of each sampling site and soil characteristics at the sample map. 3.2 Soil Testing Data This dataset includes basic information about the soil itself like pH, percentage of organic matter, variety of soil metal concentrations. The complete data dictionary is available here. The dataset is available at the BioDIGS website. This dataset was generated by the Delaware Soil Testing Program at the University of Delaware. 3.3 Genomics and Metagenomics Data You can access this data in both raw and processed forms. The Illumina and Nanopore sequences were generated at the Johns Hopkins University Genetic Resources Core Facility. PacBio sequencing was done by PacBio directly. More information coming soon! "],["billing.html", "Chapter 4 Billing 4.1 Create Google Billing Account 4.2 Add Terra to Google Billing Account 4.3 Add Members to Google Billing Account 4.4 Set Alerts for Google Billing 4.5 View Spend for Google Billing 4.6 Create Terra Billing Project 4.7 Add Member to Terra Billing Project 4.8 Disable Terra Billing Project", " Chapter 4 Billing In order to use AnVIL, you will need to set up a billing account and add members to it. These sections guide you through that process. 4.1 Create Google Billing Account Log in to the Google Cloud Platform console using your Google ID. Make sure to use the same Google account ID you use to log into Terra. If you are a first time user, don’t forget to claim your free credits! If you haven’t been to the console before, once you accept the Terms of Service you will be greeted with an invitation to “Try for Free.” Follow the instructions to sign up for a Billing Account and get your credits. Choose “Individual Account”. This “billing account” is just for managing billing, so you don’t need to be able to add your team members. You will need to give either a credit card or bank account for security. Don’t worry! You won’t be billed until you explicitly turn on automatic billing. You can view and edit your new Billing Account, by selecting “Billing” from the left-hand menu, or going directly to the billing console console.cloud.google.com/billing Clicking on the Billing Account name will allow you to manage the account, including accessing reports, setting alerts, and managing payments and billing. At any point, you can create additional Billing Accounts using the Create Account button. We generally recommend creating a new Billing Account for each funding source. 4.2 Add Terra to Google Billing Account This gives Terra permission to create projects and send charges to the Google Billing Account, and must be done by an administrator of the Google Billing Account. Terra needs to be added as a “Billing Account User”: Log in to the Google Cloud Platform console using your Google ID. Navigate to Billing You may be automatically directed to view a specific Billing Account. If you see information about a single account rather than a list of your Billing Accounts, you can get back to the list by clicking “Manage Billing Accounts” from the drop-down menu. Check the box next to the Billing Account you wish to add Terra to, click “ADD MEMBER”. Enter terra-billing@terra.bio in the text box. In the drop-down menu, mouse over Billing, then choose “Billing Account User”. Click “SAVE”. 4.3 Add Members to Google Billing Account Anyone you wish to add to the Billing Account will need their own Google ID. To add a member to a Billing Project: Log in to the Google Cloud Platform console using your Google ID. Navigate to Billing You may be automatically directed to view a specific Billing Account. If you see information about a single account rather than a list of your Billing Accounts, you can get back to the list by clicking “Manage Billing Accounts” from the drop-down menu. Check the box next to the Billing Account you wish to add a member to, click “ADD MEMBER”. Enter their Google ID in the text box. In the drop-down menu, mouse over Billing, then choose the appropriate role. Click “SAVE”. 4.4 Set Alerts for Google Billing Log in to the Google Cloud Platform console using the Google ID associated with your Google Cloud projects. Open the dropdown menu on the top left and click on Billing. You may be automatically directed to view a specific Billing Account. If you see information about a single account (and it’s not the one you’re interested in), you can get back to the list of all your Billing Accounts by clicking “Manage Billing Accounts” from the drop-down menu. Click on the name of the Billing Account you want to set alerts for. In the left-hand menu, click “Budgets &amp; alerts”. Click the “Create Budget” tab. Enter a name for your budget, and then choose which projects you want to monitor. Then click “Next”. For Budget Type, select “Specified amount”. Enter the total budget amount for the month (you will set alerts at different thresholds in the next step). Click “Next” (do not click “Finish”). Enter the threshold amounts where you want to receive an alert. We recommend starting with 50% and 90%. You can set other alerts if you prefer. Check the box for “Email alerts to billing admins and users”, then click “Finish”. Now you (as the owner and admin), along with anyone you added with admin or user privileges (e.g. lab managers) will receive alerts when your lab members reach the specified spending thresholds. These emails will be sent to the Gmail accounts associated with the Billing Account. You can edit your budgets at any time by going to Billing &gt; Budgets &amp; alerts, and clicking on the name of the budget you want to edit. 4.5 View Spend for Google Billing You can always check your current spend through the Google Billing console, but remember There is a reporting delay (~1 day), so you cannot immediately see what an analysis cost Costs are reported at the level of Workspaces, so if there are multiple people using a Workspace, you will not be able to determine which of them was responsible for the charges. The Google Billing console displays information by Billing Account. To view spending: Log in to the Google Cloud Platform console using the Google ID associated with your Google Cloud projects. Open the dropdown menu on the top left and click on Billing. You may be automatically directed to view a specific Billing Account. If you see information about a single account (and it’s not the one you’re interested in), you can get back to the list of all your Billing Accounts by clicking “Manage Billing Accounts” from the drop-down menu. Click on the name of the Billing Account for the project you want to view. Look at the top of the Overview tab to see your month-to-date spending. Scroll further down the Overview tab to show your top projects. Click on the Reports tab to see more detailed information about each of your projects. This is probably the most useful tab for exploring costs of individual projects over time. Click on the Cost table tab to obtain a convenient table of spending per project. 4.6 Create Terra Billing Project Launch Terra and sign in with your Google account. If this is your first time logging in to Terra, you will need to accept the Terms of Service. In the drop-down menu on the left, navigate to “Billing”. Click the triple bar in the top left corner to access the menu. Click the arrow next to your name to expand the menu, then click “Billing”. You can also navigate there directly with this link: https://anvil.terra.bio/#billing On the Billing page, click the “+ CREATE” button to create a new Billing Project. If prompted, select the Google account to use. If prompted, give Terra permission to manage Google Cloud Platform billing accounts. Enter a unique name for your Terra Billing Project and select the appropriate Google Billing Account. The name of the Terra Billing Project must: Only contain lowercase letters, numbers and hyphens Start with a lowercase letter Not end with a hyphen Be between 6 and 30 characters Select the Google Billing Account to use. All activities conducted under your new Terra Billing Project will charge to this Google Billing Account. If prompted, give Terra permission to manage Google Cloud Platform billing accounts. Click “CREATE BILLING PROJECT”. Your new Billing Project should now show up in the list of Billing Projects Owned by You. You can add additional members or can modify or deactivate the Billing Project at any time by clicking on its name in this list. The page doesn’t always update as soon as the Billing Project is created. If it’s been a couple of minutes and you don’t see a change, try refreshing the page. 4.7 Add Member to Terra Billing Project Launch Terra and sign in with your Google account. In the drop-down menu on the left, navigate to “Billing”. Click the triple bar in the top left corner to access the menu. Click the arrow next to your name to expand the menu, then click “Billing”. You can also navigate there directly with this link: https://anvil.terra.bio/#billing Click “Owned by You” and find the Billing Project. If you do not see the Billing Project in this list, then you are not an Owner and do not have permission to add members. Click on the name of the Billing Project. Click on the “Members” tab to view and manage members. Then click the “Add User” button. Enter the email address of the user or group you’d like to add the the Billing Project. If adding an individual, make sure to enter the account that they use to access AnVIL. If adding a Terra Group, use the Group email address, which can be found on the Terra Group management page. If this user or group will need to add and remove other users of the Billing Project, check the Owner box. Otherwise leave it unchecked. It’s often a good idea to have at least one other Owner of a Billing Project in order to avoid getting locked out, in case the original owner leaves or loses access to their account. Click “ADD USER”. You should now see the user or group listed in the Billing Project members, along with the appropriate role. They should now be able to use the Billing Project to fund work on AnVIL. If you need to remove members or modify their roles, you can do so at any time by clicking the teardrop button next to their name. 4.8 Disable Terra Billing Project By default this module includes a warning to make sure people understand they will lose access to their Workspace buckets. You can remove the warning from this module by setting AnVIL_module_settings$warning to FALSE before running cow::borrow_chapter: AnVIL_module_settings &lt;- list( warning = FALSE ) cow::borrow_chapter( doc_path = &quot;child/_child_terra_billing_project_disable.Rmd&quot;, repo_name = &quot;jhudsl/AnVIL_Template&quot; ) Disabling a Billing Project makes Workspace contents inaccessible! Disabling a Billing Project disables funding to all Workspaces funded by the Billing Project. You will be unable to compute in these Workspaces, and you will lose access to any data stored in the Workspace buckets. It is sometimes possible to restore access by reactivating billing, but Google makes no promises about whether or how long the data will be recoverable. Make sure everyone with Workspaces funded by the Billing Project has saved anything they want to keep in another location before disabling the Billing Project. To disable a Terra Billing Project (i.e. remove the Google Billing Account that funds the Terra Billing Project): Launch Terra and sign in with your Google account. In the drop-down menu on the left, navigate to “Billing”. Click the triple bar in the top left corner to access the menu. Click the arrow next to your name to expand the menu, then click “Billing”. You can also navigate there directly with this link: https://anvil.terra.bio/#billing Click “Owned by You” and find the Billing Project. If you do not see the Billing Project in this list, then you are not an Owner and do not have permission to add members. Click on the name of the Billing Project. If you don’t see information about the Billing Account, click on “View billing account” to expand the Billing Account information. You may be prompted to enter your login information again. You should see the name of the Google Billing Account that is funding this Terra Billing Project. Click on the teardrop icon next to the name of the Billing Account. Click “Remove Billing Account”. Click OK to confirm that you want to disable funding for this Billing Project. The page should now indicate that there is no linked billing account. If necessary, you can restore funding to the Billing Project and associated Workspaces by clicking the teardrop icon and selecting “Change Billing Account”. However, Google makes no promises about how long the Workspace contents will remain available after you disable funding, so it is best not to rely on them. "],["anvil-workspace.html", "Chapter 5 AnVIL Workspace 5.1 Create Google Account 5.2 Clone the Workspace", " Chapter 5 AnVIL Workspace You can easily access the data on AnVIL by cloning the dedicated workspace. These sections guide you through creating an AnVIL account and accessing the workspace. 5.1 Create Google Account If you do not already have a Google account that you would like to use for accessing Terra, create one now. If you would like to create a Google account that is associated with your non-Gmail, institutional email address, follow these instructions. 5.2 Clone the Workspace Launch Terra Locate the Workspace you want to clone. If a Workspace has been shared with you ahead of time, it will appear in “MY WORKSPACES”. You can clone a Workspace that was shared with you to perform your own analyses. In the screenshot below, no Workspaces have been shared. If a Workspace hasn’t been shared with you, navigate to the “FEATURED” or “PUBLIC” Workspace tabs. Use the search box to find the Workspace you want to clone. Click the teardrop button on the far right next to the Workspace you want to clone. Click “Clone”. You can also clone the Workspace from the Workspace Dashboard instead of the search results. You will see a popup box appear. Name your Workspace and select the appropriate Terra Billing Project. All activity in the Workspace will be charged to this Billing Project (regardless of who conducted it). Remember that each Workspace should have its own Billing Project. If you are working with protected data, you can set the Authorization Domain to limit who can be added to your Workspace. Note that the Authorization Domain cannot be changed after the Workspace is created (i.e. there is no way to make this Workspace shareable with a larger audience in the future). Workspaces by default are only visible to people you specifically share them with. Authorization domains add an extra layer of enforcement over privacy, but by nature make sharing more complicated. We recommend using Authorization Domains in cases where it is extremely important and/or legally required that the data be kept private (e.g. protected patient data, industry data). For data you would merely prefer not be shared with the world, we recommend relying on standard Workspace sharing permissions rather than Authorization Domains, as Authorization Domains can make future collaborations, publications, or other sharing complicated. Click “CLONE WORKSPACE”. The new Workspace should now show up under your Workspaces. "],["programming-platforms.html", "Chapter 6 Programming Platforms 6.1 Video overview on using Jupyter Notebooks 6.2 Launching Jupyter 6.3 Video overview on using Galaxy 6.4 Starting Galaxy 6.5 Navigating Galaxy 6.6 Deleting Galaxy 6.7 Video overview on using RStudio 6.8 Launching RStudio 6.9 Touring RStudio 6.10 Pausing RStudio 6.11 Deleting RStudio", " Chapter 6 Programming Platforms These sections provide a general overview of how to use RStudio and Galaxy on AnVIL. 6.1 Video overview on using Jupyter Notebooks Here is a video tutorial that describes the basics of using Jupyter Notebook on AnVIL. 6.1.1 Objectives Start compute for your Jupyter environment Create notebook to perform analysis Stop compute to minimize expenses 6.1.2 Slides The slides for this tutorial are are located here. 6.2 Launching Jupyter AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select a cloud computing environment appropriate to your needs to avoid runaway costs. If you are uncertain, start with the default settings; it is fairly easy to increase your compute resources later, if needed, but harder to scale down. Note that, in order to use Jupyter, you must have access to a Terra Workspace with permission to compute (i.e. you must be a “Writer” or “Owner” of the Workspace). Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under Jupyter. You will see some configuration options for the Jupyter cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. Configure any settings you need for your cloud environment. If you are uncertain about what you need, the default configuration is a reasonable, cost-conservative choice. It is fairly easy to increase your compute resources later, if needed, but harder to scale down. Scroll down and click the “CREATE” button when you are satisfied with your setup. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the Jupyter icon. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the “ANALYSES” tab to create or open a Jupyter Notebook. From the ANALYSES tab, you can click on the name of an existing Jupyter Notebook to view and launch it, or click the “START” button to create a new Notebook. Clicking on a Notebook name will open a static preview of the Notebook. To edit and run the Notebook, click the “OPEN” button. 6.3 Video overview on using Galaxy Here is a video tutorial that describes the basics of using Galaxy on AnVIL. 6.3.1 Objectives Start compute for your Galaxy on AnVIL Run tool to quality control sequencing reads Stop compute to minimize expenses 6.3.2 Slides The slides for this tutorial are are located here. 6.4 Starting Galaxy Note that, in order to use Galaxy, you must have access to a Terra Workspace with permission to compute (i.e. you must be a “Writer” or “Owner” of the Workspace). Open your Workspace, and click on the “NOTEBOOKS” tab. Next, click on “Create a Cloud Environment for Galaxy”. You should see a popup window on the right side of the screen. Click on “NEXT” and “CREATE” to keep all settings as-is. This will take 8-10 minutes. When it is done, click “LAUNCH GALAXY”. 6.5 Navigating Galaxy Notice the three main sections. Tools - These are all of the bioinformatics tool packages available for you to use. The Main Dashboard - This contains flash messages and posts when you first open Galaxy, but when we are using data this is the main interface area. History - When you start a project you will be able to see all of the documents in the project in the history. Now be aware, this can become very busy. Also the naming that Galaxy uses is not very intuitive, so you must make sure that you label your files with something that makes sense to you. On the welcome page, there are links to tutorials. You may try these out on your own. If you want to try a new analysis this is a good place to start. 6.6 Deleting Galaxy Once you are done with your activity, you’ll need to shut down your Galaxy cloud environment. This frees up the cloud resources for others and minimizes computing cost. The following steps will delete your work, so make sure you are completely finished at this point. Otherwise, you will have to repeat your work from the previous steps. Return to AnVIL, and find the Galaxy logo that shows your cloud environment is running. Click on this logo: Next, click on “DELETE ENVIRONMENT OPTIONS”: Finally, select “Delete everything, including persistent disk”. Make sure you are done with the activity and then click “DELETE”. 6.7 Video overview on using RStudio Here is a video tutorial that describes the basics of using RStudio on AnVIL. 6.7.1 Objectives Start compute for your RStudio environment Tour RStudio on AnVIL Stop compute to minimize expenses 6.7.2 Slides The slides for this tutorial are are located here. 6.8 Launching RStudio AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select a cloud computing environment appropriate to your needs to avoid runaway costs. If you are uncertain, start with the default settings; it is fairly easy to increase your compute resources later, if needed, but harder to scale down. Note that, in order to use RStudio, you must have access to a Terra Workspace with permission to compute (i.e. you must be a “Writer” or “Owner” of the Workspace). Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under RStudio. You will see some details about the default RStudio cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. If you are uncertain about what you need, the default configuration is a reasonable, cost-conservative choice. It is fairly easy to increase your compute resources later, if needed, but harder to scale down. Click the “Create” button. Otherwise, click “CUSTOMIZE” to modify the environment for your needs. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the RStudio logo. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the RStudio logo to open a new dialogue box that will let you launch RStudio. Click the launch icon to open RStudio. This is also where you can pause, modify, or delete your environment when needed. You should now see the RStudio interface with information about the version printed to the console. 6.9 Touring RStudio Next, we will be using RStudio and the package Glimma to create interactive plots. See this vignette for more information. The Bioconductor team has created a very useful package to programmatically interact with Terra and Google Cloud. Install the AnVIL package. It will make some steps easier as we go along. You can now quickly install precompiled binaries using the AnVIL package’s install() function. We will use it to install the Glimma package and the airway package. The airway package contains a SummarizedExperiment data class. This data describes an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. {Note: for some of the packages, you will have to install packaged from the CRAN repository, using the install.packages() function. The examples will show you which install method to use.} &lt;img src=&quot;06-using_platforms_modules_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g11f12bc99af_0_56.png&quot; title=&quot;Screenshot of the RStudio environment interface. Code has been typed in the console and is highlighted.&quot; alt=&quot;Screenshot of the RStudio environment interface. Code has been typed in the console and is highlighted.&quot; width=&quot;100%&quot; /&gt; Load the example data. The multidimensional scaling (MDS) plot is frequently used to explore differences in samples. When this data is MDS transformed, the first two dimensions explain the greatest variance between samples, and the amount of variance decreases monotonically with increasing dimension. The following code will launch a new window where you can interact with the MDS plot. Change the colour_by setting to “groups” so you can easily distinguish between groups. In this data, the “group” is the treatment. You can download the interactive html file by clicking on “Save As”. You can also download plots and other files created directly in RStudio. To download the following plot, click on “Export” and save in your preferred format to the default directory. This saves the file in your cloud environment. You should see the plot in the “Files” pane. Select this file and click “More” &gt; “Export” Select “Download” to save the file to your local machine. 6.10 Pausing RStudio The right-hand side icon reminds you that you are accruing cloud computing costs. If you don’t see this icon, you may need to scroll to the right. You should minimize charges when you are not performing an analysis. You can do this by clicking on the RStudio icon and selecting “Pause”. This will release the CPU and memory resources for other people to use. Note that your work will be saved in the environment and continue to accrue a very small cost. This work will be lost if the cloud environment gets deleted. If there is anything you would like to save permanently, it’s a good idea to copy it from your compute environment to another location, such as the Workspace bucket, GitHub, or your local machine, depending on your needs. You can also pause your cloud environment(s) at https://anvil.terra.bio/#clusters. 6.11 Deleting RStudio Pausing your cloud environment only temporarily stops your work. When you are ready to delete the cloud environment, click on the RStudio icon on the right-hand side and select “Settings”. If you don’t see this icon, you may need to scroll to the right. Click on “Delete Environment”. If you are certain that you do not need the data and configuration on your disk, you should select “Delete everything, including persistent disk”. If there is anything you would like to save, open the compute environment and copy the file(s) from your compute environment to another location, such as the Workspace bucket, GitHub, or your local machine, depending on your needs. Select “DELETE”. You can also delete your cloud environment(s) and disk storage at https://anvil.terra.bio/#clusters. "],["instructor-guide.html", "Chapter 7 Instructor Guide", " Chapter 7 Instructor Guide "],["student-guide.html", "Chapter 8 Student Guide 8.1 Student Account Setup 8.2 Student instructions for cloning a Workspace 8.3 Student instructions for launching Jupyter 8.4 Student instructions for launching RStudio", " Chapter 8 Student Guide Modules aimed at students in a course or workshop. 8.1 Student Account Setup In order to run your analyses, you will use the AnVIL cloud computing platform, so that you do not need to install everything on your own computer. The AnVIL (Analysis Visualization and Informatics Lab-space) platform is specially designed for analyzing biological data, and is used by scientists doing all sorts of biological research. AnVIL in a nutshell Behind the scenes, AnVIL relies on Google Cloud Platform to provide computing infrastructure. Basically, AnVIL lets you “rent” computers from Google (remotely). Whenever you run an analyses on AnVIL, it actually runs on one of Google’s computers, and AnVIL lets you see the results in your browser. AnVIL uses Terra to provide many computational tools useful for biological data analysis, such as RStudio, Galaxy, and Jupyter Notebooks. Terra takes care of installing these tools on Google’s computers, so that you can just start using them. 8.1.1 Create Google Account First, you will need to set up a (free) Google account. If you do not already have a Google account that you would like to use for accessing AnVIL, create one now. Alternatively, if you would like to create a Google account that is associated with an existing non-Gmail email address, you can follow these instructions. 8.1.2 Log In to Terra Next, make sure you can log in to Terra – you will use Terra to perform computations on AnVIL. You can access Terra by going to anvil.terra.bio, or by clicking the link on the AnVIL home page. Open Terra, and you should be prompted to sign in with your Google account. 8.1.3 Share Username Finally, make sure your instructor has your Google account username (e.g. myname@gmail.com), so they can give you access to everything you need. Make sure there are no typos! If you have multiple Google accounts, make sure you give them the username that you will be using to access AnVIL It is very important that you share the Google account you will be using to access AnVIL with with your instructor! Otherwise, the instructor cannot add you to Billing Projects or Workspaces, and you will be unable to proceed with your assignments. 8.2 Student instructions for cloning a Workspace These instructions can be customized to a specific workspace by setting certain variables before running cow::borrow_chapter(). If these variables have not been set, reasonable defaults are provided (e.g. “ask your instructor”). 8.2.1 With no variables set: This will not work until your instructor has given you permission to spend money to “rent” the computers that will power your analyses (by adding you to a “Billing Project”). On AnVIL, you access files and computers through Workspaces. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment. This will give you access to the files you will need (data, code) the computing environment you will use Tip At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other. To clone an AnVIL Workspace: Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. You are automatically directed to the “MY WORKSPACES” tab. Here you can see any Workspaces that have been shared with you, along with your permission level. Depending on how your instructor has set things up, you may or may not see any Workspaces in this tab. Locate the Workspace specified by your instructor. (The images below show the SARS-CoV-2-Genome Workspace as an example, but you should look for the Workspace specified by your instructor.) If it has been shared with you ahead of time, it will appear in “MY WORKSPACES”. Otherwise, select the “PUBLIC” tab. In the top search bar, type the Workspace name specified by your instructor. You can also go directly to the Workspace by clicking this link: ask your instructor. Clone the workspace by clicking the teardrop button (). Select “Clone”. Or, if you have opened the Workspace, you can find the teardrop button on the top right of the Workspace. You will see a popup box appear, asking you to configure your Workspace Give your Workspace clone a name by adding an underscore (“_“) and your name. For example, \"ExampleWorkspace_Firstname_Lastname\". Select the Billing Project provided by your instructor. Leave the bottom two boxes as-is. Click “CLONE WORKSPACE”. The new Workspace should now show up under “MY WORKSPACES”. You now have your own copy of the Workspace to work in. 8.2.2 With variables set: This will not work until your instructor has given you permission to spend money to “rent” the computers that will power your analyses (by adding you to a “Billing Project”). On AnVIL, you access files and computers through Workspaces. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment. This will give you access to the files you will need (data, code) the computing environment you will use Tip At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other. To clone an AnVIL Workspace: Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. You are automatically directed to the “MY WORKSPACES” tab. Here you can see any Workspaces that have been shared with you, along with your permission level. Depending on how your instructor has set things up, you may or may not see any Workspaces in this tab. Locate the Workspace Example_Workspace. (The images below show the SARS-CoV-2-Genome Workspace as an example, but you should look for the Workspace Example_Workspace.) If it has been shared with you ahead of time, it will appear in “MY WORKSPACES”. Otherwise, select the “PUBLIC” tab. In the top search bar, type the Workspace name Example_Workspace. You can also go directly to the Workspace by clicking this link: http://example.com/. Clone the workspace by clicking the teardrop button (). Select “Clone”. Or, if you have opened the Workspace, you can find the teardrop button on the top right of the Workspace. You will see a popup box appear, asking you to configure your Workspace Give your Workspace clone a name by adding an underscore (“_“) and your name. For example, \"Example_Workspace_Firstname_Lastname\". Select the Billing Project Example Billing Project. Leave the bottom two boxes as-is. Click “CLONE WORKSPACE”. The new Workspace should now show up under “MY WORKSPACES”. You now have your own copy of the Workspace to work in. 8.3 Student instructions for launching Jupyter The module below is specially customized for students, allowing you to give more specific instructions on the settings for their Jupyter environment. There are several other general purpose modules that may also be useful for students (e.g. Pausing Jupyter, Deleting Jupyter) that can be found in other chapters of this book. The following instructions can be customized by setting certain variables before running cow::borrow_chapter(). Developers should create these variables as a list AnVIL_module_settings. The following variables can be provided: audience = Defaults to general, telling them to use the default Jupyter settings. If audience is set to student, it gives more specific instructions. docker_image = Optional, it will tell them how to set the image. startup_script = Optional, it will tell them how to set the script. 8.3.1 Using default Jupyter environment: AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs. Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under Jupyter. You will see some configuration options for the Jupyter cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. Leave everything else as-is. To create your Jupyter Cloud Environment, scroll down and click the “CREATE” button. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the Jupyter icon. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the “ANALYSES” tab to create or open a Jupyter Notebook. From the ANALYSES tab, you can click on the name of an existing Jupyter Notebook to view and launch it, or click the “START” button to create a new Notebook. 8.3.2 Using custom Jupyter environment: AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs. Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under Jupyter. You will see some configuration options for the Jupyter cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. Under “Application configuration” you will see a dropdown menu. Choose “Custom Environment”. Then copy the following link into “Container image” textbox: example docker Under “Startup script” you will see textbox. Copy the following link into the box: example startup script Leave everything else as-is. To create your Jupyter Cloud Environment, scroll down and click the “CREATE” button. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the Jupyter icon. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the “ANALYSES” tab to create or open a Jupyter Notebook. From the ANALYSES tab, you can click on the name of an existing Jupyter Notebook to view and launch it, or click the “START” button to create a new Notebook. 8.4 Student instructions for launching RStudio The module below is specially customized for students, allowing you to give more specific instructions on the settings for their RStudio environment. There are several other general purpose modules that may also be useful for students (e.g. Pausing RStudio, Deleting RStudio) that can be found in other chapters of this book. The following instructions can be customized by setting certain variables before running cow::borrow_chapter(). Developers should create these variables as a list AnVIL_module_settings. The following variables can be provided: audience = Defaults to general, telling them to use the default RStudio settings. If audience is set to student, it gives more specific instructions. docker_image = Optional, it will tell them to open the customization dialogue and direct them on how to set the image. startup_script = Optional, it will tell them to open the customization dialogue and direct them on how to set the script. 8.4.1 Using default RStudio environment: AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs. Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under RStudio. You will see some details about the default RStudio cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. Click the “CREATE” button. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the RStudio logo. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the RStudio logo to open a new dialogue box that will let you launch RStudio. Click the launch icon to open RStudio. This is also where you can pause, modify, or delete your environment when needed. You should now see the RStudio interface with information about the version printed to the console. 8.4.2 Using custom RStudio environment: AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs. Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under RStudio. You will see some details about the default RStudio cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. Click “CUSTOMIZE” to adjust the settings for your environment. Under “Application configuration” you will see a dropdown menu. You can also enter text here. Copy the following link into the box: example docker Under “Startup script” you will see textbox. Copy the following link into the box: example startup script Leave everything else as-is. To create your RStudio Cloud Environment, click on the “CREATE” button. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the RStudio logo. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the RStudio logo to open a new dialogue box that will let you launch RStudio. Click the launch icon to open RStudio. This is also where you can pause, modify, or delete your environment when needed. You should now see the RStudio interface with information about the version printed to the console. "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Pedagogy Lead Content Instructor(s) FirstName LastName Lecturer(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved Delivered the course in some way - video or audio Content Author(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved If any other authors besides lead instructor Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involved Wrote less than a chapter AnVIL instructions: Katherine Cox, Ava Hoffman, Elizabeth Humphries Content Editor(s)/Reviewer(s) Checked your content Content Director(s) Helped guide the content direction Content Consultants (include chapter name/link in parentheses or word “General”) - make new line if more than one chapter involved Gave high level advice on content AnVIL instructions: Allie Cliffe Acknowledgments Gave small assistance to content but not to the level of consulting Production Content Publisher(s) Helped with publishing platform Content Publishing Reviewer(s) Reviewed overall content and aesthetics on publishing platform Technical Course Publishing Engineer(s) Helped with the code for the technical aspects related to the specific course generation Template Publishing Engineers Candace Savonen, Carrie Wright Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Candace Savonen Package Developers (ottrpal) John Muschelli, Candace Savonen, Carrie Wright Art and Design Illustrator(s) Created graphics for the course Figure Artist(s) Created figures/plots for course Videographer(s) Filmed videos Videography Editor(s) Edited film Audiographer(s) Recorded audio Audiography Editor(s) Edited audio recordings Funding Funder(s) Institution/individual who funded course including grant number Funding Staff Staff members who help with funding   ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.0.2 (2020-06-22) ## os Ubuntu 20.04.5 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-02-02 ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date lib source ## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.5) ## bookdown 0.24 2023-03-28 [1] Github (rstudio/bookdown@88bc4ea) ## bslib 0.4.2 2022-12-16 [1] CRAN (R 4.0.2) ## cachem 1.0.7 2023-02-24 [1] CRAN (R 4.0.2) ## callr 3.5.0 2020-10-08 [1] RSPM (R 4.0.2) ## cli 3.6.1 2023-03-23 [1] CRAN (R 4.0.2) ## crayon 1.3.4 2017-09-16 [1] RSPM (R 4.0.0) ## desc 1.2.0 2018-05-01 [1] RSPM (R 4.0.3) ## devtools 2.3.2 2020-09-18 [1] RSPM (R 4.0.3) ## digest 0.6.25 2020-02-23 [1] RSPM (R 4.0.0) ## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3) ## evaluate 0.20 2023-01-17 [1] CRAN (R 4.0.2) ## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.0.2) ## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3) ## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.5) ## htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.0.2) ## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2) ## jsonlite 1.7.1 2020-09-07 [1] RSPM (R 4.0.2) ## knitr 1.33 2023-03-28 [1] Github (yihui/knitr@a1052d1) ## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.0.2) ## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2) ## pkgbuild 1.1.0 2020-07-13 [1] RSPM (R 4.0.2) ## pkgload 1.1.0 2020-05-29 [1] RSPM (R 4.0.3) ## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3) ## processx 3.4.4 2020-09-03 [1] RSPM (R 4.0.2) ## ps 1.4.0 2020-10-07 [1] RSPM (R 4.0.2) ## R6 2.4.1 2019-11-12 [1] RSPM (R 4.0.0) ## remotes 2.2.0 2020-07-21 [1] RSPM (R 4.0.3) ## rlang 1.1.0 2023-03-14 [1] CRAN (R 4.0.2) ## rmarkdown 2.10 2023-03-28 [1] Github (rstudio/rmarkdown@02d3c25) ## rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.0.2) ## sass 0.4.5 2023-01-24 [1] CRAN (R 4.0.2) ## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3) ## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3) ## stringr 1.4.0 2019-02-10 [1] RSPM (R 4.0.3) ## testthat 3.0.1 2023-03-28 [1] Github (R-lib/testthat@e99155a) ## usethis 1.6.3 2020-09-17 [1] RSPM (R 4.0.2) ## withr 2.3.0 2020-09-22 [1] RSPM (R 4.0.2) ## xfun 0.26 2023-03-28 [1] Github (yihui/xfun@74c2a66) ## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library "],["references.html", "Chapter 9 References", " Chapter 9 References "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). 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+[["index.html", "GDSCN Book: BioDIGS in the Classroom About this Book 0.1 Target Audience 0.2 Platform 0.3 Data", " GDSCN Book: BioDIGS in the Classroom February 02, 2024 About this Book This is a companion training guide for BioDIGS, a GDSCN project that brings a research experience into the classroom. Visit the BioDIGS (BioDiversity and Informatics for Genomics Scholars) website here for more information about this collaborative, distributed research project, including how you can get involved! The GDSCN (Genomics Data Science Community Network) is a consortium of educators who aim to create a world where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. You can find more information about its mission and initiatives here. BioDIGS logo 0.1 Target Audience The activities in this guide are written for undergraduate students and beginning graduate students. Some sections require basic understanding of the R programming language, which is indicated at the beginning of the chapter. 0.2 Platform The activities in this guide are demonstrated on NHGRI’s AnVIL cloud computing platform. AnVIL is the preferred computing platform for the GDSCN. However, all of these activities can be done using your personal installation of R or using the online Galaxy portal. 0.3 Data The data generated by the BioDIGS project is available through the BioDIGS website, as well as through an AnVIL workspace. Data about the soil itself as well as soil metal content was generated by the Delaware Soil Testing Program at the University of Delaware. Sequences were generated by the Johns Hopkins University Genetic Resources Core Facility and by PacBio. "],["background.html", "Chapter 1 Background 1.1 What is genomics? 1.2 What is data science? 1.3 What is cloud computing? 1.4 Why soil microbes? 1.5 Heavy metals and human health", " Chapter 1 Background One critical aspect of an undergraduate STEM education is hands-on research. Undergraduate research experiences enhance what students learn in the classroom as well as increase a student’s interest in pursuing STEM careers (Russell, Hancock, and McCullough 2007). It can also lead to improved scientific reasoning and increased academic performance overall (Buffalari et al. 2020). However, many students at underresourced institutions like community colleges, Historically Black Colleges and Universities (HBCUs), tribal colleges and universities, and Hispanic-serving institutions have limited access to research opportunities compared to their cohorts at larger four-year colleges and R1 institutions. These students are also more likely to belong to groups that are already under-represented in STEM disciplines, particularly genomics and data science (Canner et al. 2017; GDSCN 2022). The BioDIGS Project aims to be at the intersection of genomics, data science, cloud computing, and education. 1.1 What is genomics? Genomics broadly refers to the study of genomes, which are an organism’s complete set of DNA. This includes both genes and non-coding regions of DNA. Traditional genomics involves sequencing and analyzing the genome of individual species. Metagenomics expands genomics to look at the collective genomes of entire communities of organisms in an environmental sample, like soil. It allows researchers to study not just the genes of culturable or isolated organisms, but the entirety of genetic material present in a given environment. By using genomic techniques to survey the soil microbes, we can identify everything in the soil, including microbes that no one has identified before. We are doing both traditional genomics and metagenomics as part of BioDIGS. 1.2 What is data science? Data science is an interdisciplinary field that uses scientific methods, processes, algorithms and systems to extract knowledge and insights from structured and unstructured data. It includes collecting, cleaning, and combining data from multiple databases, exploring data and developing statistical and machine learning models to identify patterns in complex datasets, and creating tools to efficiently store, process, and access large amounts of data. 1.3 What is cloud computing? Cloud computing just means using the internet to get access to powerful computer resources like storage, servers, databases, networking tools, and specialized software programs. Instead of having to buy and maintain their own powerful computers, storage servers, and other systems, users can pay to use them through an internet connection as needed. Users only pay for what they need, when they actually use it, and professionals update and maintain the systems in large data centers. It is a particularly useful tool for researchers and students at smaller institutions with limited computational services, especially when working with complex databases. The genome assembly and analyses for BioDIGS have been done using the NHGRI AnVIL cloud computing platform, as well as Galaxy. 1.4 Why soil microbes? It can be challenging to include undergraduates in human genomic and health research, especially in a classroom context. Both human genetic data and human health data are protected data, which limits the sort of information students can access without undergoing specialized ethics training. However, the same sorts of data cleaning and analysis methods used for human genomic data are also used for microbial genomic data, which does not have the same sort of legal protections as human genetic data. This makes it ideal for training undergraduate students at the beginning of their careers and can be used to prepare students for future research in human genomics and health (Jurkowski, Reid, and Labov 2017). Additionally, the microbes in the soil can have big impacts on our health (Brevik and Burgess 2014). 1.5 Heavy metals and human health Human activities that change the landscape can also change what sorts of inorganic and abiotic compounds we find in the soil, particularly increasing the amount of heavy metals (Yan et al. 2020). When cars drive on roads, compounds from the exhaust, oil, and other fluids might settle onto the roads and be washed into the soil. When we put salt on roads, parking lots, and sidewalks, the salts themselves will eventually be washed away and enter the ecosystem through both water and soil. Chemicals from factories and other businesses also leech into our environment. Previous research has demonstrated that in areas with more human activity, like cities, soils include greater concentrations of heavy metals than found in rural areas with limited human populations (Khan et al. 2023; Wang, Birch, and Liu 2022). Increased heavy metal concentrations also disproportionately affect lower-income and predominantly minority areas (Jones et al. 2022). Research suggests that increased heavy metal concentration in soils has major impacts on the soil microbial community. In particular, increased heavy metal concentration is associated with an increase in soil bacteria that have antibiotic resistance markers (Gorovtsov, Sazykin, and Sazykina 2018; Nguyen et al. 2019; Sun, Xu, and Fan 2021). "],["research-team.html", "Chapter 2 Research Team 2.1 Soil sampling", " Chapter 2 Research Team This project is coordinated by the Genomics Data Science Community Network (GDSCN). You can read more about the GDSCN and its mission at the network website. 2.1 Soil sampling This map shows the current sampling locations for the BioDIGS project. The extensive network of the GDSCN has made this data collection possible. Soil sampling for this project was done by both faculty and student volunteers from schools that aren’t traditional R1 research institutions. Many of the faculty are also members of the GDSCN. This list of locations reflects GDSCN institutions and friends of GDSCN who have collected soil samples. Annandale, VA: Northern Virginia Community College Atlanta, GA: Spelman College Baltimore, MD: College of Southern Maryland, Notre Dame College of Maryland, Towson University Bismark, ND: United Tribes Technical College El Paso, TX: El Paso Community College, The University of Texas at El Paso Fresno, CA: Clovis Community College Greensboro, NC: North Carolina A&amp;T State University Harrisonburg, VA: James Madison University Honolulu, Hawai’i: University of Hawai’i at Mānoa Las Cruces, NM: Doña Ana Community College Montgomery County, MD: Montgomery College, Towson University Nashville, TN: Meharry Medical College New York, NY: Guttman Community College CUNY Petersburg, VA: Virginia State University Seattle, WA: North Seattle College, Pierce College Tsaile, AZ: Diné College "],["support.html", "Chapter 3 Support 3.1 Funding 3.2 Sponsors 3.3 Analytical and Computational Support", " Chapter 3 Support This project would not be possible without financial and technical support from many organizations and people. 3.1 Funding Funding for this project has been provided by the National Human Genome Research Institute (Contract # 75N92022P00232 awarded to Johns Hopkins University). 3.2 Sponsors PacBio and CosmosID have graciously donated supplies. Advances in Genome Biology and Technology provided funding support for several team members to attend AGBT 2024. 3.3 Analytical and Computational Support Computational support has been provided by NHGRI’s AnVIL cloud computing platform and Galaxy. "],["data-1.html", "Chapter 4 Data 4.1 Sample Metadata 4.2 Soil Testing Data 4.3 Genomics and Metagenomics Data", " Chapter 4 Data There are currently three major kinds of data available from BioDIGS: sample metadata, soil testing data, and genomics and metagenomics data. All of these are available for use in your classroom. 4.1 Sample Metadata This dataset contains information about the samples themselves, including GPS coordinates for the sample location, date the sample was taken, and the site name. This dataset is also available from the BioDIGS website You can also see images of each sampling site and soil characteristics at the sample map. 4.2 Soil Testing Data This dataset includes basic information about the soil itself like pH, percentage of organic matter, variety of soil metal concentrations. The complete data dictionary is available here. The dataset is available at the BioDIGS website. This dataset was generated by the Delaware Soil Testing Program at the University of Delaware. 4.3 Genomics and Metagenomics Data You can access this data in both raw and processed forms. The Illumina and Nanopore sequences were generated at the Johns Hopkins University Genetic Resources Core Facility. PacBio sequencing was done by PacBio directly. More information coming soon! "],["billing.html", "Chapter 5 Billing 5.1 Create Google Billing Account 5.2 Add Terra to Google Billing Account 5.3 Add Members to Google Billing Account 5.4 Set Alerts for Google Billing 5.5 View Spend for Google Billing 5.6 Create Terra Billing Project 5.7 Add Member to Terra Billing Project 5.8 Disable Terra Billing Project", " Chapter 5 Billing In order to use AnVIL, you will need to set up a billing account and add members to it. These sections guide you through that process. 5.1 Create Google Billing Account Log in to the Google Cloud Platform console using your Google ID. Make sure to use the same Google account ID you use to log into Terra. If you are a first time user, don’t forget to claim your free credits! If you haven’t been to the console before, once you accept the Terms of Service you will be greeted with an invitation to “Try for Free.” Follow the instructions to sign up for a Billing Account and get your credits. Choose “Individual Account”. This “billing account” is just for managing billing, so you don’t need to be able to add your team members. You will need to give either a credit card or bank account for security. Don’t worry! You won’t be billed until you explicitly turn on automatic billing. You can view and edit your new Billing Account, by selecting “Billing” from the left-hand menu, or going directly to the billing console console.cloud.google.com/billing Clicking on the Billing Account name will allow you to manage the account, including accessing reports, setting alerts, and managing payments and billing. At any point, you can create additional Billing Accounts using the Create Account button. We generally recommend creating a new Billing Account for each funding source. 5.2 Add Terra to Google Billing Account This gives Terra permission to create projects and send charges to the Google Billing Account, and must be done by an administrator of the Google Billing Account. Terra needs to be added as a “Billing Account User”: Log in to the Google Cloud Platform console using your Google ID. Navigate to Billing You may be automatically directed to view a specific Billing Account. If you see information about a single account rather than a list of your Billing Accounts, you can get back to the list by clicking “Manage Billing Accounts” from the drop-down menu. Check the box next to the Billing Account you wish to add Terra to, click “ADD MEMBER”. Enter terra-billing@terra.bio in the text box. In the drop-down menu, mouse over Billing, then choose “Billing Account User”. Click “SAVE”. 5.3 Add Members to Google Billing Account Anyone you wish to add to the Billing Account will need their own Google ID. To add a member to a Billing Project: Log in to the Google Cloud Platform console using your Google ID. Navigate to Billing You may be automatically directed to view a specific Billing Account. If you see information about a single account rather than a list of your Billing Accounts, you can get back to the list by clicking “Manage Billing Accounts” from the drop-down menu. Check the box next to the Billing Account you wish to add a member to, click “ADD MEMBER”. Enter their Google ID in the text box. In the drop-down menu, mouse over Billing, then choose the appropriate role. Click “SAVE”. 5.4 Set Alerts for Google Billing Log in to the Google Cloud Platform console using the Google ID associated with your Google Cloud projects. Open the dropdown menu on the top left and click on Billing. You may be automatically directed to view a specific Billing Account. If you see information about a single account (and it’s not the one you’re interested in), you can get back to the list of all your Billing Accounts by clicking “Manage Billing Accounts” from the drop-down menu. Click on the name of the Billing Account you want to set alerts for. In the left-hand menu, click “Budgets &amp; alerts”. Click the “Create Budget” tab. Enter a name for your budget, and then choose which projects you want to monitor. Then click “Next”. For Budget Type, select “Specified amount”. Enter the total budget amount for the month (you will set alerts at different thresholds in the next step). Click “Next” (do not click “Finish”). Enter the threshold amounts where you want to receive an alert. We recommend starting with 50% and 90%. You can set other alerts if you prefer. Check the box for “Email alerts to billing admins and users”, then click “Finish”. Now you (as the owner and admin), along with anyone you added with admin or user privileges (e.g. lab managers) will receive alerts when your lab members reach the specified spending thresholds. These emails will be sent to the Gmail accounts associated with the Billing Account. You can edit your budgets at any time by going to Billing &gt; Budgets &amp; alerts, and clicking on the name of the budget you want to edit. 5.5 View Spend for Google Billing You can always check your current spend through the Google Billing console, but remember There is a reporting delay (~1 day), so you cannot immediately see what an analysis cost Costs are reported at the level of Workspaces, so if there are multiple people using a Workspace, you will not be able to determine which of them was responsible for the charges. The Google Billing console displays information by Billing Account. To view spending: Log in to the Google Cloud Platform console using the Google ID associated with your Google Cloud projects. Open the dropdown menu on the top left and click on Billing. You may be automatically directed to view a specific Billing Account. If you see information about a single account (and it’s not the one you’re interested in), you can get back to the list of all your Billing Accounts by clicking “Manage Billing Accounts” from the drop-down menu. Click on the name of the Billing Account for the project you want to view. Look at the top of the Overview tab to see your month-to-date spending. Scroll further down the Overview tab to show your top projects. Click on the Reports tab to see more detailed information about each of your projects. This is probably the most useful tab for exploring costs of individual projects over time. Click on the Cost table tab to obtain a convenient table of spending per project. 5.6 Create Terra Billing Project Launch Terra and sign in with your Google account. If this is your first time logging in to Terra, you will need to accept the Terms of Service. In the drop-down menu on the left, navigate to “Billing”. Click the triple bar in the top left corner to access the menu. Click the arrow next to your name to expand the menu, then click “Billing”. You can also navigate there directly with this link: https://anvil.terra.bio/#billing On the Billing page, click the “+ CREATE” button to create a new Billing Project. If prompted, select the Google account to use. If prompted, give Terra permission to manage Google Cloud Platform billing accounts. Enter a unique name for your Terra Billing Project and select the appropriate Google Billing Account. The name of the Terra Billing Project must: Only contain lowercase letters, numbers and hyphens Start with a lowercase letter Not end with a hyphen Be between 6 and 30 characters Select the Google Billing Account to use. All activities conducted under your new Terra Billing Project will charge to this Google Billing Account. If prompted, give Terra permission to manage Google Cloud Platform billing accounts. Click “CREATE BILLING PROJECT”. Your new Billing Project should now show up in the list of Billing Projects Owned by You. You can add additional members or can modify or deactivate the Billing Project at any time by clicking on its name in this list. The page doesn’t always update as soon as the Billing Project is created. If it’s been a couple of minutes and you don’t see a change, try refreshing the page. 5.7 Add Member to Terra Billing Project Launch Terra and sign in with your Google account. In the drop-down menu on the left, navigate to “Billing”. Click the triple bar in the top left corner to access the menu. Click the arrow next to your name to expand the menu, then click “Billing”. You can also navigate there directly with this link: https://anvil.terra.bio/#billing Click “Owned by You” and find the Billing Project. If you do not see the Billing Project in this list, then you are not an Owner and do not have permission to add members. Click on the name of the Billing Project. Click on the “Members” tab to view and manage members. Then click the “Add User” button. Enter the email address of the user or group you’d like to add the the Billing Project. If adding an individual, make sure to enter the account that they use to access AnVIL. If adding a Terra Group, use the Group email address, which can be found on the Terra Group management page. If this user or group will need to add and remove other users of the Billing Project, check the Owner box. Otherwise leave it unchecked. It’s often a good idea to have at least one other Owner of a Billing Project in order to avoid getting locked out, in case the original owner leaves or loses access to their account. Click “ADD USER”. You should now see the user or group listed in the Billing Project members, along with the appropriate role. They should now be able to use the Billing Project to fund work on AnVIL. If you need to remove members or modify their roles, you can do so at any time by clicking the teardrop button next to their name. 5.8 Disable Terra Billing Project By default this module includes a warning to make sure people understand they will lose access to their Workspace buckets. You can remove the warning from this module by setting AnVIL_module_settings$warning to FALSE before running cow::borrow_chapter: AnVIL_module_settings &lt;- list( warning = FALSE ) cow::borrow_chapter( doc_path = &quot;child/_child_terra_billing_project_disable.Rmd&quot;, repo_name = &quot;jhudsl/AnVIL_Template&quot; ) Disabling a Billing Project makes Workspace contents inaccessible! Disabling a Billing Project disables funding to all Workspaces funded by the Billing Project. You will be unable to compute in these Workspaces, and you will lose access to any data stored in the Workspace buckets. It is sometimes possible to restore access by reactivating billing, but Google makes no promises about whether or how long the data will be recoverable. Make sure everyone with Workspaces funded by the Billing Project has saved anything they want to keep in another location before disabling the Billing Project. To disable a Terra Billing Project (i.e. remove the Google Billing Account that funds the Terra Billing Project): Launch Terra and sign in with your Google account. In the drop-down menu on the left, navigate to “Billing”. Click the triple bar in the top left corner to access the menu. Click the arrow next to your name to expand the menu, then click “Billing”. You can also navigate there directly with this link: https://anvil.terra.bio/#billing Click “Owned by You” and find the Billing Project. If you do not see the Billing Project in this list, then you are not an Owner and do not have permission to add members. Click on the name of the Billing Project. If you don’t see information about the Billing Account, click on “View billing account” to expand the Billing Account information. You may be prompted to enter your login information again. You should see the name of the Google Billing Account that is funding this Terra Billing Project. Click on the teardrop icon next to the name of the Billing Account. Click “Remove Billing Account”. Click OK to confirm that you want to disable funding for this Billing Project. The page should now indicate that there is no linked billing account. If necessary, you can restore funding to the Billing Project and associated Workspaces by clicking the teardrop icon and selecting “Change Billing Account”. However, Google makes no promises about how long the Workspace contents will remain available after you disable funding, so it is best not to rely on them. "],["anvil-workspace.html", "Chapter 6 AnVIL Workspace 6.1 Create Google Account 6.2 Clone the Workspace", " Chapter 6 AnVIL Workspace You can easily access the data on AnVIL by cloning the dedicated workspace. These sections guide you through creating an AnVIL account and accessing the workspace. 6.1 Create Google Account If you do not already have a Google account that you would like to use for accessing Terra, create one now. If you would like to create a Google account that is associated with your non-Gmail, institutional email address, follow these instructions. 6.2 Clone the Workspace Launch Terra Locate the Workspace you want to clone. If a Workspace has been shared with you ahead of time, it will appear in “MY WORKSPACES”. You can clone a Workspace that was shared with you to perform your own analyses. In the screenshot below, no Workspaces have been shared. If a Workspace hasn’t been shared with you, navigate to the “FEATURED” or “PUBLIC” Workspace tabs. Use the search box to find the Workspace you want to clone. Click the teardrop button on the far right next to the Workspace you want to clone. Click “Clone”. You can also clone the Workspace from the Workspace Dashboard instead of the search results. You will see a popup box appear. Name your Workspace and select the appropriate Terra Billing Project. All activity in the Workspace will be charged to this Billing Project (regardless of who conducted it). Remember that each Workspace should have its own Billing Project. If you are working with protected data, you can set the Authorization Domain to limit who can be added to your Workspace. Note that the Authorization Domain cannot be changed after the Workspace is created (i.e. there is no way to make this Workspace shareable with a larger audience in the future). Workspaces by default are only visible to people you specifically share them with. Authorization domains add an extra layer of enforcement over privacy, but by nature make sharing more complicated. We recommend using Authorization Domains in cases where it is extremely important and/or legally required that the data be kept private (e.g. protected patient data, industry data). For data you would merely prefer not be shared with the world, we recommend relying on standard Workspace sharing permissions rather than Authorization Domains, as Authorization Domains can make future collaborations, publications, or other sharing complicated. Click “CLONE WORKSPACE”. The new Workspace should now show up under your Workspaces. "],["programming-platforms.html", "Chapter 7 Programming Platforms 7.1 Video overview on using Jupyter Notebooks 7.2 Launching Jupyter 7.3 Video overview on using Galaxy 7.4 Starting Galaxy 7.5 Navigating Galaxy 7.6 Deleting Galaxy 7.7 Video overview on using RStudio 7.8 Launching RStudio 7.9 Touring RStudio 7.10 Pausing RStudio 7.11 Deleting RStudio", " Chapter 7 Programming Platforms These sections provide a general overview of how to use RStudio and Galaxy on AnVIL. 7.1 Video overview on using Jupyter Notebooks Here is a video tutorial that describes the basics of using Jupyter Notebook on AnVIL. 7.1.1 Objectives Start compute for your Jupyter environment Create notebook to perform analysis Stop compute to minimize expenses 7.1.2 Slides The slides for this tutorial are are located here. 7.2 Launching Jupyter AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select a cloud computing environment appropriate to your needs to avoid runaway costs. If you are uncertain, start with the default settings; it is fairly easy to increase your compute resources later, if needed, but harder to scale down. Note that, in order to use Jupyter, you must have access to a Terra Workspace with permission to compute (i.e. you must be a “Writer” or “Owner” of the Workspace). Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under Jupyter. You will see some configuration options for the Jupyter cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. Configure any settings you need for your cloud environment. If you are uncertain about what you need, the default configuration is a reasonable, cost-conservative choice. It is fairly easy to increase your compute resources later, if needed, but harder to scale down. Scroll down and click the “CREATE” button when you are satisfied with your setup. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the Jupyter icon. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the “ANALYSES” tab to create or open a Jupyter Notebook. From the ANALYSES tab, you can click on the name of an existing Jupyter Notebook to view and launch it, or click the “START” button to create a new Notebook. Clicking on a Notebook name will open a static preview of the Notebook. To edit and run the Notebook, click the “OPEN” button. 7.3 Video overview on using Galaxy Here is a video tutorial that describes the basics of using Galaxy on AnVIL. 7.3.1 Objectives Start compute for your Galaxy on AnVIL Run tool to quality control sequencing reads Stop compute to minimize expenses 7.3.2 Slides The slides for this tutorial are are located here. 7.4 Starting Galaxy Note that, in order to use Galaxy, you must have access to a Terra Workspace with permission to compute (i.e. you must be a “Writer” or “Owner” of the Workspace). Open your Workspace, and click on the “NOTEBOOKS” tab. Next, click on “Create a Cloud Environment for Galaxy”. You should see a popup window on the right side of the screen. Click on “NEXT” and “CREATE” to keep all settings as-is. This will take 8-10 minutes. When it is done, click “LAUNCH GALAXY”. 7.5 Navigating Galaxy Notice the three main sections. Tools - These are all of the bioinformatics tool packages available for you to use. The Main Dashboard - This contains flash messages and posts when you first open Galaxy, but when we are using data this is the main interface area. History - When you start a project you will be able to see all of the documents in the project in the history. Now be aware, this can become very busy. Also the naming that Galaxy uses is not very intuitive, so you must make sure that you label your files with something that makes sense to you. On the welcome page, there are links to tutorials. You may try these out on your own. If you want to try a new analysis this is a good place to start. 7.6 Deleting Galaxy Once you are done with your activity, you’ll need to shut down your Galaxy cloud environment. This frees up the cloud resources for others and minimizes computing cost. The following steps will delete your work, so make sure you are completely finished at this point. Otherwise, you will have to repeat your work from the previous steps. Return to AnVIL, and find the Galaxy logo that shows your cloud environment is running. Click on this logo: Next, click on “DELETE ENVIRONMENT OPTIONS”: Finally, select “Delete everything, including persistent disk”. Make sure you are done with the activity and then click “DELETE”. 7.7 Video overview on using RStudio Here is a video tutorial that describes the basics of using RStudio on AnVIL. 7.7.1 Objectives Start compute for your RStudio environment Tour RStudio on AnVIL Stop compute to minimize expenses 7.7.2 Slides The slides for this tutorial are are located here. 7.8 Launching RStudio AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select a cloud computing environment appropriate to your needs to avoid runaway costs. If you are uncertain, start with the default settings; it is fairly easy to increase your compute resources later, if needed, but harder to scale down. Note that, in order to use RStudio, you must have access to a Terra Workspace with permission to compute (i.e. you must be a “Writer” or “Owner” of the Workspace). Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under RStudio. You will see some details about the default RStudio cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. If you are uncertain about what you need, the default configuration is a reasonable, cost-conservative choice. It is fairly easy to increase your compute resources later, if needed, but harder to scale down. Click the “Create” button. Otherwise, click “CUSTOMIZE” to modify the environment for your needs. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the RStudio logo. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the RStudio logo to open a new dialogue box that will let you launch RStudio. Click the launch icon to open RStudio. This is also where you can pause, modify, or delete your environment when needed. You should now see the RStudio interface with information about the version printed to the console. 7.9 Touring RStudio Next, we will be using RStudio and the package Glimma to create interactive plots. See this vignette for more information. The Bioconductor team has created a very useful package to programmatically interact with Terra and Google Cloud. Install the AnVIL package. It will make some steps easier as we go along. You can now quickly install precompiled binaries using the AnVIL package’s install() function. We will use it to install the Glimma package and the airway package. The airway package contains a SummarizedExperiment data class. This data describes an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. {Note: for some of the packages, you will have to install packaged from the CRAN repository, using the install.packages() function. The examples will show you which install method to use.} &lt;img src=&quot;06-using_platforms_modules_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g11f12bc99af_0_56.png&quot; title=&quot;Screenshot of the RStudio environment interface. Code has been typed in the console and is highlighted.&quot; alt=&quot;Screenshot of the RStudio environment interface. Code has been typed in the console and is highlighted.&quot; width=&quot;100%&quot; /&gt; Load the example data. The multidimensional scaling (MDS) plot is frequently used to explore differences in samples. When this data is MDS transformed, the first two dimensions explain the greatest variance between samples, and the amount of variance decreases monotonically with increasing dimension. The following code will launch a new window where you can interact with the MDS plot. Change the colour_by setting to “groups” so you can easily distinguish between groups. In this data, the “group” is the treatment. You can download the interactive html file by clicking on “Save As”. You can also download plots and other files created directly in RStudio. To download the following plot, click on “Export” and save in your preferred format to the default directory. This saves the file in your cloud environment. You should see the plot in the “Files” pane. Select this file and click “More” &gt; “Export” Select “Download” to save the file to your local machine. 7.10 Pausing RStudio The right-hand side icon reminds you that you are accruing cloud computing costs. If you don’t see this icon, you may need to scroll to the right. You should minimize charges when you are not performing an analysis. You can do this by clicking on the RStudio icon and selecting “Pause”. This will release the CPU and memory resources for other people to use. Note that your work will be saved in the environment and continue to accrue a very small cost. This work will be lost if the cloud environment gets deleted. If there is anything you would like to save permanently, it’s a good idea to copy it from your compute environment to another location, such as the Workspace bucket, GitHub, or your local machine, depending on your needs. You can also pause your cloud environment(s) at https://anvil.terra.bio/#clusters. 7.11 Deleting RStudio Pausing your cloud environment only temporarily stops your work. When you are ready to delete the cloud environment, click on the RStudio icon on the right-hand side and select “Settings”. If you don’t see this icon, you may need to scroll to the right. Click on “Delete Environment”. If you are certain that you do not need the data and configuration on your disk, you should select “Delete everything, including persistent disk”. If there is anything you would like to save, open the compute environment and copy the file(s) from your compute environment to another location, such as the Workspace bucket, GitHub, or your local machine, depending on your needs. Select “DELETE”. You can also delete your cloud environment(s) and disk storage at https://anvil.terra.bio/#clusters. "],["instructor-guide.html", "Chapter 8 Instructor Guide", " Chapter 8 Instructor Guide "],["student-guide.html", "Chapter 9 Student Guide 9.1 Student Account Setup 9.2 Student instructions for cloning a Workspace 9.3 Student instructions for launching Jupyter 9.4 Student instructions for launching RStudio", " Chapter 9 Student Guide Modules aimed at students in a course or workshop. 9.1 Student Account Setup In order to run your analyses, you will use the AnVIL cloud computing platform, so that you do not need to install everything on your own computer. The AnVIL (Analysis Visualization and Informatics Lab-space) platform is specially designed for analyzing biological data, and is used by scientists doing all sorts of biological research. AnVIL in a nutshell Behind the scenes, AnVIL relies on Google Cloud Platform to provide computing infrastructure. Basically, AnVIL lets you “rent” computers from Google (remotely). Whenever you run an analyses on AnVIL, it actually runs on one of Google’s computers, and AnVIL lets you see the results in your browser. AnVIL uses Terra to provide many computational tools useful for biological data analysis, such as RStudio, Galaxy, and Jupyter Notebooks. Terra takes care of installing these tools on Google’s computers, so that you can just start using them. 9.1.1 Create Google Account First, you will need to set up a (free) Google account. If you do not already have a Google account that you would like to use for accessing AnVIL, create one now. Alternatively, if you would like to create a Google account that is associated with an existing non-Gmail email address, you can follow these instructions. 9.1.2 Log In to Terra Next, make sure you can log in to Terra – you will use Terra to perform computations on AnVIL. You can access Terra by going to anvil.terra.bio, or by clicking the link on the AnVIL home page. Open Terra, and you should be prompted to sign in with your Google account. 9.1.3 Share Username Finally, make sure your instructor has your Google account username (e.g. myname@gmail.com), so they can give you access to everything you need. Make sure there are no typos! If you have multiple Google accounts, make sure you give them the username that you will be using to access AnVIL It is very important that you share the Google account you will be using to access AnVIL with with your instructor! Otherwise, the instructor cannot add you to Billing Projects or Workspaces, and you will be unable to proceed with your assignments. 9.2 Student instructions for cloning a Workspace These instructions can be customized to a specific workspace by setting certain variables before running cow::borrow_chapter(). If these variables have not been set, reasonable defaults are provided (e.g. “ask your instructor”). 9.2.1 With no variables set: This will not work until your instructor has given you permission to spend money to “rent” the computers that will power your analyses (by adding you to a “Billing Project”). On AnVIL, you access files and computers through Workspaces. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment. This will give you access to the files you will need (data, code) the computing environment you will use Tip At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other. To clone an AnVIL Workspace: Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. You are automatically directed to the “MY WORKSPACES” tab. Here you can see any Workspaces that have been shared with you, along with your permission level. Depending on how your instructor has set things up, you may or may not see any Workspaces in this tab. Locate the Workspace specified by your instructor. (The images below show the SARS-CoV-2-Genome Workspace as an example, but you should look for the Workspace specified by your instructor.) If it has been shared with you ahead of time, it will appear in “MY WORKSPACES”. Otherwise, select the “PUBLIC” tab. In the top search bar, type the Workspace name specified by your instructor. You can also go directly to the Workspace by clicking this link: ask your instructor. Clone the workspace by clicking the teardrop button (). Select “Clone”. Or, if you have opened the Workspace, you can find the teardrop button on the top right of the Workspace. You will see a popup box appear, asking you to configure your Workspace Give your Workspace clone a name by adding an underscore (“_“) and your name. For example, \"ExampleWorkspace_Firstname_Lastname\". Select the Billing Project provided by your instructor. Leave the bottom two boxes as-is. Click “CLONE WORKSPACE”. The new Workspace should now show up under “MY WORKSPACES”. You now have your own copy of the Workspace to work in. 9.2.2 With variables set: This will not work until your instructor has given you permission to spend money to “rent” the computers that will power your analyses (by adding you to a “Billing Project”). On AnVIL, you access files and computers through Workspaces. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment. This will give you access to the files you will need (data, code) the computing environment you will use Tip At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other. To clone an AnVIL Workspace: Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. You are automatically directed to the “MY WORKSPACES” tab. Here you can see any Workspaces that have been shared with you, along with your permission level. Depending on how your instructor has set things up, you may or may not see any Workspaces in this tab. Locate the Workspace Example_Workspace. (The images below show the SARS-CoV-2-Genome Workspace as an example, but you should look for the Workspace Example_Workspace.) If it has been shared with you ahead of time, it will appear in “MY WORKSPACES”. Otherwise, select the “PUBLIC” tab. In the top search bar, type the Workspace name Example_Workspace. You can also go directly to the Workspace by clicking this link: http://example.com/. Clone the workspace by clicking the teardrop button (). Select “Clone”. Or, if you have opened the Workspace, you can find the teardrop button on the top right of the Workspace. You will see a popup box appear, asking you to configure your Workspace Give your Workspace clone a name by adding an underscore (“_“) and your name. For example, \"Example_Workspace_Firstname_Lastname\". Select the Billing Project Example Billing Project. Leave the bottom two boxes as-is. Click “CLONE WORKSPACE”. The new Workspace should now show up under “MY WORKSPACES”. You now have your own copy of the Workspace to work in. 9.3 Student instructions for launching Jupyter The module below is specially customized for students, allowing you to give more specific instructions on the settings for their Jupyter environment. There are several other general purpose modules that may also be useful for students (e.g. Pausing Jupyter, Deleting Jupyter) that can be found in other chapters of this book. The following instructions can be customized by setting certain variables before running cow::borrow_chapter(). Developers should create these variables as a list AnVIL_module_settings. The following variables can be provided: audience = Defaults to general, telling them to use the default Jupyter settings. If audience is set to student, it gives more specific instructions. docker_image = Optional, it will tell them how to set the image. startup_script = Optional, it will tell them how to set the script. 9.3.1 Using default Jupyter environment: AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs. Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under Jupyter. You will see some configuration options for the Jupyter cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. Leave everything else as-is. To create your Jupyter Cloud Environment, scroll down and click the “CREATE” button. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the Jupyter icon. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the “ANALYSES” tab to create or open a Jupyter Notebook. From the ANALYSES tab, you can click on the name of an existing Jupyter Notebook to view and launch it, or click the “START” button to create a new Notebook. 9.3.2 Using custom Jupyter environment: AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs. Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under Jupyter. You will see some configuration options for the Jupyter cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. Under “Application configuration” you will see a dropdown menu. Choose “Custom Environment”. Then copy the following link into “Container image” textbox: example docker Under “Startup script” you will see textbox. Copy the following link into the box: example startup script Leave everything else as-is. To create your Jupyter Cloud Environment, scroll down and click the “CREATE” button. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the Jupyter icon. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the “ANALYSES” tab to create or open a Jupyter Notebook. From the ANALYSES tab, you can click on the name of an existing Jupyter Notebook to view and launch it, or click the “START” button to create a new Notebook. 9.4 Student instructions for launching RStudio The module below is specially customized for students, allowing you to give more specific instructions on the settings for their RStudio environment. There are several other general purpose modules that may also be useful for students (e.g. Pausing RStudio, Deleting RStudio) that can be found in other chapters of this book. The following instructions can be customized by setting certain variables before running cow::borrow_chapter(). Developers should create these variables as a list AnVIL_module_settings. The following variables can be provided: audience = Defaults to general, telling them to use the default RStudio settings. If audience is set to student, it gives more specific instructions. docker_image = Optional, it will tell them to open the customization dialogue and direct them on how to set the image. startup_script = Optional, it will tell them to open the customization dialogue and direct them on how to set the script. 9.4.1 Using default RStudio environment: AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs. Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under RStudio. You will see some details about the default RStudio cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. Click the “CREATE” button. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the RStudio logo. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the RStudio logo to open a new dialogue box that will let you launch RStudio. Click the launch icon to open RStudio. This is also where you can pause, modify, or delete your environment when needed. You should now see the RStudio interface with information about the version printed to the console. 9.4.2 Using custom RStudio environment: AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs. Open Terra - use a web browser to go to anvil.terra.bio In the drop-down menu on the left, navigate to “Workspaces”. Click the triple bar in the top left corner to access the menu. Click “Workspaces”. Click on the name of your Workspace. You should be routed to a link that looks like: https://anvil.terra.bio/#workspaces/&lt;billing-project&gt;/&lt;workspace-name&gt;. Click on the cloud icon on the far right to access your Cloud Environment options. In the dialogue box, click the “Settings” button under RStudio. You will see some details about the default RStudio cloud environment, and a list of costs because it costs a small amount of money to use cloud computing. Click “CUSTOMIZE” to adjust the settings for your environment. Under “Application configuration” you will see a dropdown menu. You can also enter text here. Copy the following link into the box: example docker Under “Startup script” you will see textbox. Copy the following link into the box: example startup script Leave everything else as-is. To create your RStudio Cloud Environment, click on the “CREATE” button. The dialogue box will close and you will be returned to your Workspace. You can see the status of your cloud environment by hovering over the RStudio logo. It will take a few minutes for Terra to request computers and install software. When your environment is ready, its status will change to “Running”. Click on the RStudio logo to open a new dialogue box that will let you launch RStudio. Click the launch icon to open RStudio. This is also where you can pause, modify, or delete your environment when needed. You should now see the RStudio interface with information about the version printed to the console. 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-  <title>Chapter 8 Student Guide | GDSCN Book: BioDIGS in the Classroom</title>
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-  <meta property="og:title" content="Chapter 8 Student Guide | GDSCN Book: BioDIGS in the Classroom" />
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-  <meta name="twitter:title" content="Chapter 8 Student Guide | GDSCN Book: BioDIGS in the Classroom" />
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 <li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
 <ul>
 <li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
-<li class="chapter" data-level="2.2" data-path="research-team.html"><a href="research-team.html#funding"><i class="fa fa-check"></i><b>2.2</b> Funding</a></li>
-<li class="chapter" data-level="2.3" data-path="research-team.html"><a href="research-team.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>2.3</b> Analytical and Computational Support</a></li>
 </ul></li>
-<li class="chapter" data-level="3" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>3</b> Data</a>
+<li class="chapter" data-level="3" data-path="support.html"><a href="support.html"><i class="fa fa-check"></i><b>3</b> Support</a>
 <ul>
-<li class="chapter" data-level="3.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>3.1</b> Sample Metadata</a></li>
-<li class="chapter" data-level="3.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>3.2</b> Soil Testing Data</a></li>
-<li class="chapter" data-level="3.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>3.3</b> Genomics and Metagenomics Data</a></li>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
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-<li class="chapter" data-level="4" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>4</b> Billing</a>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
 <ul>
-<li class="chapter" data-level="4.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>4.1</b> Create Google Billing Account</a></li>
-<li class="chapter" data-level="4.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>4.2</b> Add Terra to Google Billing Account</a></li>
-<li class="chapter" data-level="4.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>4.3</b> Add Members to Google Billing Account</a></li>
-<li class="chapter" data-level="4.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>4.4</b> Set Alerts for Google Billing</a></li>
-<li class="chapter" data-level="4.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>4.5</b> View Spend for Google Billing</a></li>
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-<li class="chapter" data-level="4.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>4.8</b> Disable Terra Billing Project</a></li>
+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
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-<li class="chapter" data-level="5" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>5</b> AnVIL Workspace</a>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Account</a></li>
-<li class="chapter" data-level="5.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>5.2</b> Clone the Workspace</a></li>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
 </ul></li>
-<li class="chapter" data-level="6" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>6</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
 <ul>
-<li class="chapter" data-level="6.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>6.1</b> Video overview on using Jupyter Notebooks</a>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
 <ul>
-<li class="chapter" data-level="6.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>6.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>6.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>6.2</b> Launching Jupyter</a></li>
-<li class="chapter" data-level="6.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>6.3</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="6.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>6.3.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>6.3.2</b> Slides</a></li>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>6.4</b> Starting Galaxy</a></li>
-<li class="chapter" data-level="6.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>6.5</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="6.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>6.6</b> Deleting Galaxy</a></li>
-<li class="chapter" data-level="6.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>6.7</b> Video overview on using RStudio</a>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
 <ul>
-<li class="chapter" data-level="6.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>6.7.1</b> Objectives</a></li>
-<li class="chapter" data-level="6.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>6.7.2</b> Slides</a></li>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="6.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>6.8</b> Launching RStudio</a></li>
-<li class="chapter" data-level="6.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>6.9</b> Touring RStudio</a></li>
-<li class="chapter" data-level="6.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>6.10</b> Pausing RStudio</a></li>
-<li class="chapter" data-level="6.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>6.11</b> Deleting RStudio</a></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
 </ul></li>
 <li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="7" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>7</b> Instructor Guide</a></li>
-<li class="chapter" data-level="8" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>8</b> Student Guide</a>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
 <ul>
-<li class="chapter" data-level="8.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>8.1</b> Student Account Setup</a></li>
-<li class="chapter" data-level="8.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>8.2</b> Student instructions for cloning a Workspace</a>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
 <ul>
-<li class="chapter" data-level="8.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>8.2.1</b> With no variables set:</a></li>
-<li class="chapter" data-level="8.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>8.2.2</b> With variables set:</a></li>
+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>8.3</b> Student instructions for launching Jupyter</a>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
 <ul>
-<li class="chapter" data-level="8.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>8.3.1</b> Using default Jupyter environment:</a></li>
-<li class="chapter" data-level="8.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>8.3.2</b> Using custom Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
 </ul></li>
-<li class="chapter" data-level="8.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>8.4</b> Student instructions for launching RStudio</a>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
 <ul>
-<li class="chapter" data-level="8.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>8.4.1</b> Using default RStudio environment:</a></li>
-<li class="chapter" data-level="8.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>8.4.2</b> Using custom RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
 </ul></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="9" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>9</b> References</a></li>
+<li class="chapter" data-level="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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>
@@ -233,12 +237,12 @@ <h1>
 <div class="hero-image-container">
   <img class= "hero-image" src="assets/GDSCN_style/dasl_thin_main_image.png">
 </div>
-<div id="student-guide" class="section level1" number="8">
-<h1><span class="header-section-number">Chapter 8</span> Student Guide</h1>
+<div id="student-guide" class="section level1" number="9">
+<h1><span class="header-section-number">Chapter 9</span> Student Guide</h1>
 <p>Modules aimed at students in a course or workshop.</p>
 <p><br></p>
-<div id="student-account-setup" class="section level2" number="8.1">
-<h2><span class="header-section-number">8.1</span> Student Account Setup</h2>
+<div id="student-account-setup" class="section level2" number="9.1">
+<h2><span class="header-section-number">9.1</span> Student Account Setup</h2>
 <div class="borrowed_chunk">
 <p>In order to run your analyses, you will use the <a href="https://anvilproject.org/">AnVIL cloud computing platform</a>, so that you do not need to install everything on your own computer. The AnVIL (Analysis Visualization and Informatics Lab-space) platform is specially designed for analyzing biological data, and is used by scientists doing all sorts of biological research.</p>
 <div class="notice">
@@ -248,23 +252,23 @@ <h2><span class="header-section-number">8.1</span> Student Account Setup</h2>
 <li>AnVIL uses <a href="https://anvil.terra.bio/">Terra</a> to provide many computational tools useful for biological data analysis, such as <a href="https://www.rstudio.com/products/rstudio/">RStudio</a>, <a href="https://usegalaxy.org/">Galaxy</a>, and <a href="https://jupyter.org/">Jupyter Notebooks</a>. Terra takes care of installing these tools on Google’s computers, so that you can just start using them.</li>
 </ul>
 </div>
-<div id="create-google-account-1" class="section level3" number="8.1.1">
-<h3><span class="header-section-number">8.1.1</span> Create Google Account</h3>
+<div id="create-google-account-1" class="section level3" number="9.1.1">
+<h3><span class="header-section-number">9.1.1</span> Create Google Account</h3>
 <p>First, you will need to set up a (free) Google account.</p>
 <p>If you do not already have a Google account that you would like to use for accessing AnVIL, <a href="https://accounts.google.com/SignUp">create one now</a>.</p>
 <ul>
 <li>Alternatively, if you would like to create a Google account that is associated with an existing non-Gmail email address, you can follow <a href="https://support.terra.bio/hc/en-us/articles/360029186611">these instructions</a>.</li>
 </ul>
 </div>
-<div id="log-in-to-terra" class="section level3" number="8.1.2">
-<h3><span class="header-section-number">8.1.2</span> Log In to Terra</h3>
+<div id="log-in-to-terra" class="section level3" number="9.1.2">
+<h3><span class="header-section-number">9.1.2</span> Log In to Terra</h3>
 <p>Next, make sure you can log in to Terra – you will use Terra to perform computations on AnVIL.</p>
 <p>You can access Terra by going to <a href="https://anvil.terra.bio/"><code>anvil.terra.bio</code></a>, or by clicking the link on the <a href="https://anvilproject.org/">AnVIL home page</a>.</p>
 <p><img src="resources/images/08-data_exploration_files/figure-html/1-PVlDAzmDncjcCHIy9ZyR3ROyPpfjrg46LhEQopDc1Q_g22c9add987a_0_5.png" title="Screenshot of the AnVIL home page. The section descring Terra is highlighted." alt="Screenshot of the AnVIL home page. The section descring Terra is highlighted." width="480" /></p>
 <p>Open Terra, and you should be prompted to sign in with your Google account.</p>
 </div>
-<div id="share-username" class="section level3" number="8.1.3">
-<h3><span class="header-section-number">8.1.3</span> Share Username</h3>
+<div id="share-username" class="section level3" number="9.1.3">
+<h3><span class="header-section-number">9.1.3</span> Share Username</h3>
 <p>Finally, make sure your instructor has your Google account username (e.g. <code>myname@gmail.com</code>), so they can give you access to everything you need.</p>
 <ul>
 <li>Make sure there are no typos!</li>
@@ -276,11 +280,11 @@ <h3><span class="header-section-number">8.1.3</span> Share Username</h3>
 </div>
 </div>
 </div>
-<div id="student-instructions-for-cloning-a-workspace" class="section level2" number="8.2">
-<h2><span class="header-section-number">8.2</span> Student instructions for cloning a Workspace</h2>
+<div id="student-instructions-for-cloning-a-workspace" class="section level2" number="9.2">
+<h2><span class="header-section-number">9.2</span> Student instructions for cloning a Workspace</h2>
 <p>These instructions can be customized to a specific workspace by setting certain variables before running <code>cow::borrow_chapter()</code>. If these variables have not been set, reasonable defaults are provided (e.g. “ask your instructor”).</p>
-<div id="with-no-variables-set" class="section level3" number="8.2.1">
-<h3><span class="header-section-number">8.2.1</span> With no variables set:</h3>
+<div id="with-no-variables-set" class="section level3" number="9.2.1">
+<h3><span class="header-section-number">9.2.1</span> With no variables set:</h3>
 <div class="borrowed_chunk">
 <div class="warning">
 <p>This <strong>will not work</strong> until your instructor has given you permission to spend money to “rent” the computers that will power your analyses (by adding you to a “Billing Project”).</p>
@@ -328,8 +332,8 @@ <h3><span class="header-section-number">8.2.1</span> With no variables set:</h3>
 </ol>
 </div>
 </div>
-<div id="with-variables-set" class="section level3" number="8.2.2">
-<h3><span class="header-section-number">8.2.2</span> With variables set:</h3>
+<div id="with-variables-set" class="section level3" number="9.2.2">
+<h3><span class="header-section-number">9.2.2</span> With variables set:</h3>
 <div class="borrowed_chunk">
 <div class="warning">
 <p>This <strong>will not work</strong> until your instructor has given you permission to spend money to “rent” the computers that will power your analyses (by adding you to a “Billing Project”).</p>
@@ -378,8 +382,8 @@ <h3><span class="header-section-number">8.2.2</span> With variables set:</h3>
 </div>
 </div>
 </div>
-<div id="student-instructions-for-launching-jupyter" class="section level2" number="8.3">
-<h2><span class="header-section-number">8.3</span> Student instructions for launching Jupyter</h2>
+<div id="student-instructions-for-launching-jupyter" class="section level2" number="9.3">
+<h2><span class="header-section-number">9.3</span> Student instructions for launching Jupyter</h2>
 <p>The module below is specially customized for students, allowing you to give more specific instructions on the settings for their Jupyter environment. There are several other general purpose modules that may also be useful for students (e.g. Pausing Jupyter, Deleting Jupyter) that can be found in other chapters of this book.</p>
 <p>The following instructions can be customized by setting certain variables before running <code>cow::borrow_chapter()</code>. Developers should create these variables as a list <code>AnVIL_module_settings</code>. The following variables can be provided:</p>
 <ul>
@@ -387,8 +391,8 @@ <h2><span class="header-section-number">8.3</span> Student instructions for laun
 <li><code>docker_image</code> = Optional, it will tell them how to set the image.</li>
 <li><code>startup_script</code> = Optional, it will tell them how to set the script.</li>
 </ul>
-<div id="using-default-jupyter-environment" class="section level3" number="8.3.1">
-<h3><span class="header-section-number">8.3.1</span> Using default Jupyter environment:</h3>
+<div id="using-default-jupyter-environment" class="section level3" number="9.3.1">
+<h3><span class="header-section-number">9.3.1</span> Using default Jupyter environment:</h3>
 <div class="borrowed_chunk">
 <div class="warning">
 <p>AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs.</p>
@@ -415,8 +419,8 @@ <h3><span class="header-section-number">8.3.1</span> Using default Jupyter envir
 </ol>
 </div>
 </div>
-<div id="using-custom-jupyter-environment" class="section level3" number="8.3.2">
-<h3><span class="header-section-number">8.3.2</span> Using custom Jupyter environment:</h3>
+<div id="using-custom-jupyter-environment" class="section level3" number="9.3.2">
+<h3><span class="header-section-number">9.3.2</span> Using custom Jupyter environment:</h3>
 <div class="borrowed_chunk">
 <div class="warning">
 <p>AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs.</p>
@@ -451,8 +455,8 @@ <h3><span class="header-section-number">8.3.2</span> Using custom Jupyter enviro
 </div>
 </div>
 </div>
-<div id="student-instructions-for-launching-rstudio" class="section level2" number="8.4">
-<h2><span class="header-section-number">8.4</span> Student instructions for launching RStudio</h2>
+<div id="student-instructions-for-launching-rstudio" class="section level2" number="9.4">
+<h2><span class="header-section-number">9.4</span> Student instructions for launching RStudio</h2>
 <p>The module below is specially customized for students, allowing you to give more specific instructions on the settings for their RStudio environment. There are several other general purpose modules that may also be useful for students (e.g. Pausing RStudio, Deleting RStudio) that can be found in other chapters of this book.</p>
 <p>The following instructions can be customized by setting certain variables before running <code>cow::borrow_chapter()</code>. Developers should create these variables as a list <code>AnVIL_module_settings</code>. The following variables can be provided:</p>
 <ul>
@@ -460,8 +464,8 @@ <h2><span class="header-section-number">8.4</span> Student instructions for laun
 <li><code>docker_image</code> = Optional, it will tell them to open the customization dialogue and direct them on how to set the image.</li>
 <li><code>startup_script</code> = Optional, it will tell them to open the customization dialogue and direct them on how to set the script.</li>
 </ul>
-<div id="using-default-rstudio-environment" class="section level3" number="8.4.1">
-<h3><span class="header-section-number">8.4.1</span> Using default RStudio environment:</h3>
+<div id="using-default-rstudio-environment" class="section level3" number="9.4.1">
+<h3><span class="header-section-number">9.4.1</span> Using default RStudio environment:</h3>
 <div class="borrowed_chunk">
 <div class="warning">
 <p>AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs.</p>
@@ -490,8 +494,8 @@ <h3><span class="header-section-number">8.4.1</span> Using default RStudio envir
 </ol>
 </div>
 </div>
-<div id="using-custom-rstudio-environment" class="section level3" number="8.4.2">
-<h3><span class="header-section-number">8.4.2</span> Using custom RStudio environment:</h3>
+<div id="using-custom-rstudio-environment" class="section level3" number="9.4.2">
+<h3><span class="header-section-number">9.4.2</span> Using custom RStudio environment:</h3>
 <div class="borrowed_chunk">
 <div class="warning">
 <p>AnVIL is very versatile and can scale up to use very powerful cloud computers. It’s very important that you select the cloud computing environment described here to avoid runaway costs.</p>
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+<ul class="summary">
+<a href="https://www.gdscn.org/" target="_blank"><img src="assets/GDSCN_style/logo-gdscn.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 Book</a>
+<ul>
+<li class="chapter" data-level="0.1" data-path="index.html"><a href="index.html#target-audience"><i class="fa fa-check"></i><b>0.1</b> Target Audience</a></li>
+<li class="chapter" data-level="0.2" data-path="index.html"><a href="index.html#platform"><i class="fa fa-check"></i><b>0.2</b> Platform</a></li>
+<li class="chapter" data-level="0.3" data-path="index.html"><a href="index.html#data"><i class="fa fa-check"></i><b>0.3</b> Data</a></li>
+</ul></li>
+<li class="part"><span><b>BioDIGS Overview</b></span></li>
+<li class="chapter" data-level="1" data-path="background.html"><a href="background.html"><i class="fa fa-check"></i><b>1</b> Background</a>
+<ul>
+<li class="chapter" data-level="1.1" data-path="background.html"><a href="background.html#what-is-genomics"><i class="fa fa-check"></i><b>1.1</b> What is genomics?</a></li>
+<li class="chapter" data-level="1.2" data-path="background.html"><a href="background.html#what-is-data-science"><i class="fa fa-check"></i><b>1.2</b> What is data science?</a></li>
+<li class="chapter" data-level="1.3" data-path="background.html"><a href="background.html#what-is-cloud-computing"><i class="fa fa-check"></i><b>1.3</b> What is cloud computing?</a></li>
+<li class="chapter" data-level="1.4" data-path="background.html"><a href="background.html#why-soil-microbes"><i class="fa fa-check"></i><b>1.4</b> Why soil microbes?</a></li>
+<li class="chapter" data-level="1.5" data-path="background.html"><a href="background.html#heavy-metals-and-human-health"><i class="fa fa-check"></i><b>1.5</b> Heavy metals and human health</a></li>
+</ul></li>
+<li class="chapter" data-level="2" data-path="research-team.html"><a href="research-team.html"><i class="fa fa-check"></i><b>2</b> Research Team</a>
+<ul>
+<li class="chapter" data-level="2.1" data-path="research-team.html"><a href="research-team.html#soil-sampling"><i class="fa fa-check"></i><b>2.1</b> Soil sampling</a></li>
+</ul></li>
+<li class="chapter" data-level="3" data-path="support.html"><a href="support.html"><i class="fa fa-check"></i><b>3</b> Support</a>
+<ul>
+<li class="chapter" data-level="3.1" data-path="support.html"><a href="support.html#funding"><i class="fa fa-check"></i><b>3.1</b> Funding</a></li>
+<li class="chapter" data-level="3.2" data-path="support.html"><a href="support.html#sponsors"><i class="fa fa-check"></i><b>3.2</b> Sponsors</a></li>
+<li class="chapter" data-level="3.3" data-path="support.html"><a href="support.html#analytical-and-computational-support"><i class="fa fa-check"></i><b>3.3</b> Analytical and Computational Support</a></li>
+</ul></li>
+<li class="chapter" data-level="4" data-path="data-1.html"><a href="data-1.html"><i class="fa fa-check"></i><b>4</b> Data</a>
+<ul>
+<li class="chapter" data-level="4.1" data-path="data-1.html"><a href="data-1.html#sample-metadata"><i class="fa fa-check"></i><b>4.1</b> Sample Metadata</a></li>
+<li class="chapter" data-level="4.2" data-path="data-1.html"><a href="data-1.html#soil-testing-data"><i class="fa fa-check"></i><b>4.2</b> Soil Testing Data</a></li>
+<li class="chapter" data-level="4.3" data-path="data-1.html"><a href="data-1.html#genomics-and-metagenomics-data"><i class="fa fa-check"></i><b>4.3</b> Genomics and Metagenomics Data</a></li>
+</ul></li>
+<li class="part"><span><b>Using AnVIL</b></span></li>
+<li class="chapter" data-level="5" data-path="billing.html"><a href="billing.html"><i class="fa fa-check"></i><b>5</b> Billing</a>
+<ul>
+<li class="chapter" data-level="5.1" data-path="billing.html"><a href="billing.html#create-google-billing-account"><i class="fa fa-check"></i><b>5.1</b> Create Google Billing Account</a></li>
+<li class="chapter" data-level="5.2" data-path="billing.html"><a href="billing.html#add-terra-to-google-billing-account"><i class="fa fa-check"></i><b>5.2</b> Add Terra to Google Billing Account</a></li>
+<li class="chapter" data-level="5.3" data-path="billing.html"><a href="billing.html#add-members-to-google-billing-account"><i class="fa fa-check"></i><b>5.3</b> Add Members to Google Billing Account</a></li>
+<li class="chapter" data-level="5.4" data-path="billing.html"><a href="billing.html#set-alerts-for-google-billing"><i class="fa fa-check"></i><b>5.4</b> Set Alerts for Google Billing</a></li>
+<li class="chapter" data-level="5.5" data-path="billing.html"><a href="billing.html#view-spend-for-google-billing"><i class="fa fa-check"></i><b>5.5</b> View Spend for Google Billing</a></li>
+<li class="chapter" data-level="5.6" data-path="billing.html"><a href="billing.html#create-terra-billing-project"><i class="fa fa-check"></i><b>5.6</b> Create Terra Billing Project</a></li>
+<li class="chapter" data-level="5.7" data-path="billing.html"><a href="billing.html#add-member-to-terra-billing-project"><i class="fa fa-check"></i><b>5.7</b> Add Member to Terra Billing Project</a></li>
+<li class="chapter" data-level="5.8" data-path="billing.html"><a href="billing.html#disable-terra-billing-project"><i class="fa fa-check"></i><b>5.8</b> Disable Terra Billing Project</a></li>
+</ul></li>
+<li class="chapter" data-level="6" data-path="anvil-workspace.html"><a href="anvil-workspace.html"><i class="fa fa-check"></i><b>6</b> AnVIL Workspace</a>
+<ul>
+<li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
+<li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
+</ul></li>
+<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
+<ul>
+<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a>
+<ul>
+<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
+</ul></li>
+<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-jupyter"><i class="fa fa-check"></i><b>7.2</b> Launching Jupyter</a></li>
+<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a>
+<ul>
+<li class="chapter" data-level="7.3.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-1"><i class="fa fa-check"></i><b>7.3.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.3.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-1"><i class="fa fa-check"></i><b>7.3.2</b> Slides</a></li>
+</ul></li>
+<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.5" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.5</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.6</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.7" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-rstudio"><i class="fa fa-check"></i><b>7.7</b> Video overview on using RStudio</a>
+<ul>
+<li class="chapter" data-level="7.7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives-2"><i class="fa fa-check"></i><b>7.7.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides-2"><i class="fa fa-check"></i><b>7.7.2</b> Slides</a></li>
+</ul></li>
+<li class="chapter" data-level="7.8" data-path="programming-platforms.html"><a href="programming-platforms.html#launching-rstudio"><i class="fa fa-check"></i><b>7.8</b> Launching RStudio</a></li>
+<li class="chapter" data-level="7.9" data-path="programming-platforms.html"><a href="programming-platforms.html#touring-rstudio"><i class="fa fa-check"></i><b>7.9</b> Touring RStudio</a></li>
+<li class="chapter" data-level="7.10" data-path="programming-platforms.html"><a href="programming-platforms.html#pausing-rstudio"><i class="fa fa-check"></i><b>7.10</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="7.11" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-rstudio"><i class="fa fa-check"></i><b>7.11</b> Deleting RStudio</a></li>
+</ul></li>
+<li class="part"><span><b>Data Exploration</b></span></li>
+<li class="chapter" data-level="8" data-path="instructor-guide.html"><a href="instructor-guide.html"><i class="fa fa-check"></i><b>8</b> Instructor Guide</a></li>
+<li class="chapter" data-level="9" data-path="student-guide.html"><a href="student-guide.html"><i class="fa fa-check"></i><b>9</b> Student Guide</a>
+<ul>
+<li class="chapter" data-level="9.1" data-path="student-guide.html"><a href="student-guide.html#student-account-setup"><i class="fa fa-check"></i><b>9.1</b> Student Account Setup</a></li>
+<li class="chapter" data-level="9.2" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-cloning-a-workspace"><i class="fa fa-check"></i><b>9.2</b> Student instructions for cloning a Workspace</a>
+<ul>
+<li class="chapter" data-level="9.2.1" data-path="student-guide.html"><a href="student-guide.html#with-no-variables-set"><i class="fa fa-check"></i><b>9.2.1</b> With no variables set:</a></li>
+<li class="chapter" data-level="9.2.2" data-path="student-guide.html"><a href="student-guide.html#with-variables-set"><i class="fa fa-check"></i><b>9.2.2</b> With variables set:</a></li>
+</ul></li>
+<li class="chapter" data-level="9.3" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-jupyter"><i class="fa fa-check"></i><b>9.3</b> Student instructions for launching Jupyter</a>
+<ul>
+<li class="chapter" data-level="9.3.1" data-path="student-guide.html"><a href="student-guide.html#using-default-jupyter-environment"><i class="fa fa-check"></i><b>9.3.1</b> Using default Jupyter environment:</a></li>
+<li class="chapter" data-level="9.3.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-jupyter-environment"><i class="fa fa-check"></i><b>9.3.2</b> Using custom Jupyter environment:</a></li>
+</ul></li>
+<li class="chapter" data-level="9.4" data-path="student-guide.html"><a href="student-guide.html#student-instructions-for-launching-rstudio"><i class="fa fa-check"></i><b>9.4</b> Student instructions for launching RStudio</a>
+<ul>
+<li class="chapter" data-level="9.4.1" data-path="student-guide.html"><a href="student-guide.html#using-default-rstudio-environment"><i class="fa fa-check"></i><b>9.4.1</b> Using default RStudio environment:</a></li>
+<li class="chapter" data-level="9.4.2" data-path="student-guide.html"><a href="student-guide.html#using-custom-rstudio-environment"><i class="fa fa-check"></i><b>9.4.2</b> Using custom RStudio environment:</a></li>
+</ul></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="10" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>10</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>
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+<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=GDSCN+Book:+BioDIGS+in+the+Classroom"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
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+<div id="support" class="section level1" number="3">
+<h1><span class="header-section-number">Chapter 3</span> Support</h1>
+<p>This project would not be possible without financial and technical support from many organizations and people.</p>
+<div id="funding" class="section level2" number="3.1">
+<h2><span class="header-section-number">3.1</span> Funding</h2>
+<p>Funding for this project has been provided by the <a href="https://www.genome.gov/">National Human Genome Research Institute</a> (Contract # 75N92022P00232 awarded to Johns Hopkins University).</p>
+</div>
+<div id="sponsors" class="section level2" number="3.2">
+<h2><span class="header-section-number">3.2</span> Sponsors</h2>
+<p><a href="https://www.pacb.com/">PacBio</a> and <a href="https://www.cosmosid.com/">CosmosID</a> have graciously donated supplies.</p>
+<p><a href="https://www.agbt.org/">Advances in Genome Biology and Technology</a> provided funding support for several team members to attend AGBT 2024.</p>
+</div>
+<div id="analytical-and-computational-support" class="section level2" number="3.3">
+<h2><span class="header-section-number">3.3</span> Analytical and Computational Support</h2>
+<p>Computational support has been provided by NHGRI’s <a href="https://anvilproject.org/">AnVIL</a> cloud computing platform and <a href="usegalaxy.org">Galaxy</a>.</p>
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