Render bookdown

fhdsl · Feb 2, 2024 · 284e76e · 284e76e
1 parent d818257
commit 284e76e
Show file tree

Hide file tree

Showing 97 changed files with 2,668 additions and 526 deletions.
diff --git a/docs/04-billing_modules.md b/docs/04-billing_modules.md
@@ -1,5 +1,5 @@
 
-# (PART\*) Using AnVIL {-}
+# (PART\*) AnVIL Overview {-}
 
 # Billing
 

diff --git a/docs/07-instructor_guide.md b/docs/07-instructor_guide.md
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_104.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_104.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_111.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_111.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_117.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_117.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_125.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_125.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_15.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_15.png
diff --git a/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_2.png b/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_2.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_21.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_21.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_27.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_27.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_38.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_38.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_45.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_45.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_58.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_58.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_65.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_65.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_71.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_71.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_78.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_78.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_87.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_87.png
diff --git a/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_9.png b/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_9.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_96.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g100474897dd_0_96.png
diff --git a/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_0.png b/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_0.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_10.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_10.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_132.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_132.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_24.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_24.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_301.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_301.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_315.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_315.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_327.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_327.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_344.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_344.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_356.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_356.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_365.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_365.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_378.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_378.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_386.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_386.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_39.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_39.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_394.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_394.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_54.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_54.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_70.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_70.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_90.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g1007b9b3ffb_0_90.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g10118383b73_193_0.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g10118383b73_193_0.png
diff --git a/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g10118383b73_193_8.png b/...figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_g10118383b73_193_8.png
diff --git a/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_gdb96a00840_0_138.png b/.../figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_gdb96a00840_0_138.png
diff --git a/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_gdb96a00840_0_16.png b/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_gdb96a00840_0_16.png
diff --git a/...es/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_gdb96a00840_0_6.png b/...es/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_gdb96a00840_0_6.png
diff --git a/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_gdb96a00840_0_88.png b/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_gdb96a00840_0_88.png
diff --git a/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_gdb96a00840_0_98.png b/...s/figure-html/1HHWg47Tg6miv_K7GNB6ZDTx-4Jc5IMl7APfFtD1Rqag_gdb96a00840_0_98.png
diff --git a/docs/08-student_anvil_guide.md b/docs/08-student_anvil_guide.md
diff --git a/docs/09-data_exploration.md b/docs/09-data_exploration.md
diff --git a/docs/404.html b/docs/404.html
@@ -199,7 +199,7 @@
 <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="part"><span><b>AnVIL Overview</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>
@@ -242,7 +242,7 @@
 <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>Instructor Guide</b></span></li>
+<li class="part"><span><b>Instructor Guide to AnVIL</b></span></li>
 <li class="chapter" data-level="8" data-path="notes-for-instructors.html"><a href="notes-for-instructors.html"><i class="fa fa-check"></i><b>8</b> Notes for Instructors</a></li>
 <li class="chapter" data-level="9" data-path="checklist-for-running-activities-on-anvil.html"><a href="checklist-for-running-activities-on-anvil.html"><i class="fa fa-check"></i><b>9</b> Checklist for Running Activities on AnVIL</a>
 <ul>
@@ -281,26 +281,34 @@
 <li class="chapter" data-level="11.6" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#notify-terra"><i class="fa fa-check"></i><b>11.6</b> Notify Terra</a></li>
 </ul></li>
 <li class="chapter" data-level="12" data-path="getting-credit-for-professional-development.html"><a href="getting-credit-for-professional-development.html"><i class="fa fa-check"></i><b>12</b> Getting Credit for Professional Development</a></li>
-<li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="13" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html"><i class="fa fa-check"></i><b>13</b> Exploring Soil Testing Data With R</a>
+<li class="part"><span><b>Student Guide to AnVIL</b></span></li>
+<li class="chapter" data-level="13" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html"><i class="fa fa-check"></i><b>13</b> Using RStudio on AnVIL</a>
+<ul>
+<li class="chapter" data-level="13.1" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#video-overview-of-rstudio-on-anvil"><i class="fa fa-check"></i><b>13.1</b> Video overview of RStudio on AnVIL</a>
 <ul>
-<li class="chapter" data-level="13.1" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#before-you-start"><i class="fa fa-check"></i><b>13.1</b> Before You Start</a></li>
-<li class="chapter" data-level="13.2" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#objectives-3"><i class="fa fa-check"></i><b>13.2</b> Objectives</a></li>
-<li class="chapter" data-level="13.3" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#getting-started"><i class="fa fa-check"></i><b>13.3</b> Getting Started</a>
+<li class="chapter" data-level="13.1.1" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#objectives-3"><i class="fa fa-check"></i><b>13.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="13.1.2" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#slides-3"><i class="fa fa-check"></i><b>13.1.2</b> Slides</a></li>
+</ul></li>
+<li class="chapter" data-level="13.2" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#launching-rstudio-1"><i class="fa fa-check"></i><b>13.2</b> Launching RStudio</a></li>
+<li class="chapter" data-level="13.3" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#touring-rstudio-1"><i class="fa fa-check"></i><b>13.3</b> Touring RStudio</a></li>
+<li class="chapter" data-level="13.4" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#pausing-rstudio-1"><i class="fa fa-check"></i><b>13.4</b> Pausing RStudio</a></li>
+</ul></li>
+<li class="chapter" data-level="14" data-path="using-galaxy-on-anvil.html"><a href="using-galaxy-on-anvil.html"><i class="fa fa-check"></i><b>14</b> Using Galaxy on AnVIL</a>
 <ul>
-<li class="chapter" data-level="13.3.1" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#video-overview-of-rstudio-on-anvil"><i class="fa fa-check"></i><b>13.3.1</b> Video overview of RStudio on AnVIL</a></li>
-<li class="chapter" data-level="13.3.2" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#objectives-4"><i class="fa fa-check"></i><b>13.3.2</b> Objectives</a></li>
-<li class="chapter" data-level="13.3.3" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#slides-3"><i class="fa fa-check"></i><b>13.3.3</b> Slides</a></li>
-<li class="chapter" data-level="13.3.4" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#launching-rstudio-1"><i class="fa fa-check"></i><b>13.3.4</b> Launching RStudio</a></li>
-<li class="chapter" data-level="13.3.5" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#touring-rstudio-1"><i class="fa fa-check"></i><b>13.3.5</b> Touring RStudio</a></li>
-<li class="chapter" data-level="13.3.6" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#pausing-rstudio-1"><i class="fa fa-check"></i><b>13.3.6</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="14.1" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>14.1</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="14.2" data-path="using-galaxy-on-anvil.html"><a href="using-galaxy-on-anvil.html#navigating-galaxy-1"><i class="fa fa-check"></i><b>14.2</b> Navigating Galaxy</a></li>
 </ul></li>
-<li class="chapter" data-level="13.4" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-1.-data-import"><i class="fa fa-check"></i><b>13.4</b> Part 1. Data Import</a></li>
-<li class="chapter" data-level="13.5" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-2.-data-summarization"><i class="fa fa-check"></i><b>13.5</b> Part 2. Data Summarization</a></li>
-<li class="chapter" data-level="13.6" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-3.-data-visualization"><i class="fa fa-check"></i><b>13.6</b> Part 3. Data Visualization</a></li>
+<li class="part"><span><b>Data Exploration</b></span></li>
+<li class="chapter" data-level="15" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html"><i class="fa fa-check"></i><b>15</b> Exploring Soil Testing Data With R</a>
+<ul>
+<li class="chapter" data-level="15.1" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#before-you-start"><i class="fa fa-check"></i><b>15.1</b> Before You Start</a></li>
+<li class="chapter" data-level="15.2" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#objectives-4"><i class="fa fa-check"></i><b>15.2</b> Objectives</a></li>
+<li class="chapter" data-level="15.3" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-1.-data-import"><i class="fa fa-check"></i><b>15.3</b> Part 1. Data Import</a></li>
+<li class="chapter" data-level="15.4" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-2.-data-summarization"><i class="fa fa-check"></i><b>15.4</b> Part 2. Data Summarization</a></li>
+<li class="chapter" data-level="15.5" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-3.-data-visualization"><i class="fa fa-check"></i><b>15.5</b> Part 3. Data Visualization</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="14" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>14</b> References</a></li>
+<li class="chapter" data-level="16" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>16</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
@@ -199,7 +199,7 @@
 <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="part"><span><b>AnVIL Overview</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>
@@ -242,7 +242,7 @@
 <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>Instructor Guide</b></span></li>
+<li class="part"><span><b>Instructor Guide to AnVIL</b></span></li>
 <li class="chapter" data-level="8" data-path="notes-for-instructors.html"><a href="notes-for-instructors.html"><i class="fa fa-check"></i><b>8</b> Notes for Instructors</a></li>
 <li class="chapter" data-level="9" data-path="checklist-for-running-activities-on-anvil.html"><a href="checklist-for-running-activities-on-anvil.html"><i class="fa fa-check"></i><b>9</b> Checklist for Running Activities on AnVIL</a>
 <ul>
@@ -281,26 +281,34 @@
 <li class="chapter" data-level="11.6" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#notify-terra"><i class="fa fa-check"></i><b>11.6</b> Notify Terra</a></li>
 </ul></li>
 <li class="chapter" data-level="12" data-path="getting-credit-for-professional-development.html"><a href="getting-credit-for-professional-development.html"><i class="fa fa-check"></i><b>12</b> Getting Credit for Professional Development</a></li>
-<li class="part"><span><b>Data Exploration</b></span></li>
-<li class="chapter" data-level="13" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html"><i class="fa fa-check"></i><b>13</b> Exploring Soil Testing Data With R</a>
+<li class="part"><span><b>Student Guide to AnVIL</b></span></li>
+<li class="chapter" data-level="13" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html"><i class="fa fa-check"></i><b>13</b> Using RStudio on AnVIL</a>
+<ul>
+<li class="chapter" data-level="13.1" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#video-overview-of-rstudio-on-anvil"><i class="fa fa-check"></i><b>13.1</b> Video overview of RStudio on AnVIL</a>
 <ul>
-<li class="chapter" data-level="13.1" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#before-you-start"><i class="fa fa-check"></i><b>13.1</b> Before You Start</a></li>
-<li class="chapter" data-level="13.2" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#objectives-3"><i class="fa fa-check"></i><b>13.2</b> Objectives</a></li>
-<li class="chapter" data-level="13.3" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#getting-started"><i class="fa fa-check"></i><b>13.3</b> Getting Started</a>
+<li class="chapter" data-level="13.1.1" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#objectives-3"><i class="fa fa-check"></i><b>13.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="13.1.2" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#slides-3"><i class="fa fa-check"></i><b>13.1.2</b> Slides</a></li>
+</ul></li>
+<li class="chapter" data-level="13.2" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#launching-rstudio-1"><i class="fa fa-check"></i><b>13.2</b> Launching RStudio</a></li>
+<li class="chapter" data-level="13.3" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#touring-rstudio-1"><i class="fa fa-check"></i><b>13.3</b> Touring RStudio</a></li>
+<li class="chapter" data-level="13.4" data-path="using-rstudio-on-anvil.html"><a href="using-rstudio-on-anvil.html#pausing-rstudio-1"><i class="fa fa-check"></i><b>13.4</b> Pausing RStudio</a></li>
+</ul></li>
+<li class="chapter" data-level="14" data-path="using-galaxy-on-anvil.html"><a href="using-galaxy-on-anvil.html"><i class="fa fa-check"></i><b>14</b> Using Galaxy on AnVIL</a>
 <ul>
-<li class="chapter" data-level="13.3.1" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#video-overview-of-rstudio-on-anvil"><i class="fa fa-check"></i><b>13.3.1</b> Video overview of RStudio on AnVIL</a></li>
-<li class="chapter" data-level="13.3.2" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#objectives-4"><i class="fa fa-check"></i><b>13.3.2</b> Objectives</a></li>
-<li class="chapter" data-level="13.3.3" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#slides-3"><i class="fa fa-check"></i><b>13.3.3</b> Slides</a></li>
-<li class="chapter" data-level="13.3.4" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#launching-rstudio-1"><i class="fa fa-check"></i><b>13.3.4</b> Launching RStudio</a></li>
-<li class="chapter" data-level="13.3.5" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#touring-rstudio-1"><i class="fa fa-check"></i><b>13.3.5</b> Touring RStudio</a></li>
-<li class="chapter" data-level="13.3.6" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#pausing-rstudio-1"><i class="fa fa-check"></i><b>13.3.6</b> Pausing RStudio</a></li>
+<li class="chapter" data-level="14.1" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>14.1</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="14.2" data-path="using-galaxy-on-anvil.html"><a href="using-galaxy-on-anvil.html#navigating-galaxy-1"><i class="fa fa-check"></i><b>14.2</b> Navigating Galaxy</a></li>
 </ul></li>
-<li class="chapter" data-level="13.4" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-1.-data-import"><i class="fa fa-check"></i><b>13.4</b> Part 1. Data Import</a></li>
-<li class="chapter" data-level="13.5" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-2.-data-summarization"><i class="fa fa-check"></i><b>13.5</b> Part 2. Data Summarization</a></li>
-<li class="chapter" data-level="13.6" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-3.-data-visualization"><i class="fa fa-check"></i><b>13.6</b> Part 3. Data Visualization</a></li>
+<li class="part"><span><b>Data Exploration</b></span></li>
+<li class="chapter" data-level="15" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html"><i class="fa fa-check"></i><b>15</b> Exploring Soil Testing Data With R</a>
+<ul>
+<li class="chapter" data-level="15.1" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#before-you-start"><i class="fa fa-check"></i><b>15.1</b> Before You Start</a></li>
+<li class="chapter" data-level="15.2" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#objectives-4"><i class="fa fa-check"></i><b>15.2</b> Objectives</a></li>
+<li class="chapter" data-level="15.3" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-1.-data-import"><i class="fa fa-check"></i><b>15.3</b> Part 1. Data Import</a></li>
+<li class="chapter" data-level="15.4" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-2.-data-summarization"><i class="fa fa-check"></i><b>15.4</b> Part 2. Data Summarization</a></li>
+<li class="chapter" data-level="15.5" data-path="exploring-soil-testing-data-with-r.html"><a href="exploring-soil-testing-data-with-r.html#part-3.-data-visualization"><i class="fa fa-check"></i><b>15.5</b> Part 3. Data Visualization</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="14" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>14</b> References</a></li>
+<li class="chapter" data-level="16" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>16</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>