Render bookdown

docs/02-chapter_of_course.md

@@ -225,7 +225,7 @@ devtools::session_info()
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-08-23
+##  date     2024-08-27
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
@@ -296,4 +296,3 @@ devtools::session_info()
 ## 
 ## ──────────────────────────────────────────────────────────────────────────────
 ```
-

docs/05-billing_modules.md

@@ -192,7 +192,7 @@ The Google Billing console displays information by Billing Account.  To view spe
 
     <img src="05-billing_modules_files/figure-html//1POwxqv4p6AfPHJlN9VNq0TaT44fA2RAFSpIERIMHdWU_g116f8d759be_0_2.png" alt="Screenshot of the Terra drop-down menu.  Three items are highlighted: 1) the &quot;hamburger&quot; button for extending the drop-down menu, 2) the arrow next to your username, for extending the drop-down submenu, and 3) the submenu item &quot;Billing&quot;." width="100%" />
 
-1. 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.
+1. On the Billing page, click the "+ CREATE" button to create a new Billing Project. Select GCP Billing Project (Google's Platform). If prompted, select the Google account to use and give Terra permission to manage Google Cloud Platform billing accounts.
 
     <img src="05-billing_modules_files/figure-html//1POwxqv4p6AfPHJlN9VNq0TaT44fA2RAFSpIERIMHdWU_g116f8d759be_0_149.png" alt="Screenshot of the Terra Billing Page.  The &quot;plus&quot; button next to &quot;Billing Projects&quot; is highlighted." width="100%" />
 
@@ -208,7 +208,7 @@ The Google Billing console displays information by Billing Account.  To view spe
 
     <img src="05-billing_modules_files/figure-html//1POwxqv4p6AfPHJlN9VNq0TaT44fA2RAFSpIERIMHdWU_g2105956e909_0_0.png" alt="Screenshot of the Terra Add Billing Project dialog box.  The dropdown menu labeled &quot;Select billing account&quot; is highlighted." width="100%" />
 
-1. Click "CREATE BILLING PROJECT".
+1. Click "Create".
 
     <img src="05-billing_modules_files/figure-html//1POwxqv4p6AfPHJlN9VNq0TaT44fA2RAFSpIERIMHdWU_g116f8d759be_0_438.png" alt="Screenshot of the Terra Add Billing Project dialog box.  The button labeled &quot;CREATE BILLING PROJECT&quot; is highlighted." width="100%" />
 

docs/07-using_platforms_modules.md

@@ -23,6 +23,7 @@ Here is a video tutorial that describes the basics of using Jupyter Notebook on
 ### Slides
 
 The slides for this tutorial are are located [here](https://docs.google.com/presentation/d/1GYUP874Qd7K3S0Ls6iWY_M4jywpRb53qw0f78OBCFwk).
+::::
 
 ## Launching Jupyter
 
@@ -97,7 +98,7 @@ Note that, in order to use Jupyter, you must have access to a Terra Workspace wi
 
 Here is a video tutorial that describes the basics of using Galaxy on AnVIL.
 
-<iframe src="https://drive.google.com/file/d/16QEY8x-gBsUkKEeO3w_H-I4SLIBPloXd/preview" width="640" height="360" allow="autoplay"></iframe>
+<iframe width="560" height="315" src="https://youtu.be/9TEVu7QobOo?si=tLFXNe951vVJV4iN" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 
 ### Objectives
 
@@ -107,7 +108,7 @@ Here is a video tutorial that describes the basics of using Galaxy on AnVIL.
 
 ### Slides
 
-The slides for this tutorial are are located [here](https://docs.google.com/presentation/d/1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q).
+The slides for this tutorial are are located [here](https://docs.google.com/presentation/d/1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q/edit?usp=sharing).
 ::::
 
 ## Starting Galaxy
@@ -116,9 +117,17 @@ The slides for this tutorial are are located [here](https://docs.google.com/pres
 
 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”.
+Open your Workspace, and click on the “Environment configuration” button, a cloud icon on the righthand side of the screen. 
+
+<img src="07-using_platforms_modules_files/figure-html//1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q_ge20e585f11_0_9.png" alt="Screenshot of the Workspace that points to the Environment configuration button, an icon of a cloud with a lightning bolt." width="100%" />
+
+Under Galaxy, click on “Create new Environment”. Click on “Next” and “Create” to keep all settings as-is. This will take 8-10 minutes.
+
+<img src="07-using_platforms_modules_files/figure-html//1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q_ge1182914a6_0_36.png" alt="The button that starts a cloud environment for Galaxy has been highlighted," width="100%" />
 
-<img src="07-using_platforms_modules_files/figure-html//182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_ged15532ded_0_788.png" 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%" />
+Click on "Open Galaxy" when the environment is ready.
+
+<img src="07-using_platforms_modules_files/figure-html//1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q_ge1182914a6_0_57.png" alt="The Open Galaxy button is highlighted in the ready environment popup." width="100%" />
 ::::
 
 ## Navigating Galaxy
@@ -144,17 +153,17 @@ On the welcome page, there are links to tutorials. You may try these out on your
 
 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:
+Return to AnVIL, and find the Galaxy logo that shows your cloud environment is running. Click on this logo.
 
-<img src="07-using_platforms_modules_files/figure-html//182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_gf243efded1_0_134.png" alt="Screenshot of the Workspace menu. The currently running Galaxy cloud environment logo on the top right of the page is highlighted." width="100%" />
+<img src="07-using_platforms_modules_files/figure-html//1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q_ge20e585f11_0_248.png" alt="Screenshot of the Workspace menu. The currently running Galaxy cloud environment logo on the right sidebar is highlighted." width="100%" />
 
-Next, click on “DELETE ENVIRONMENT OPTIONS”:
+Next, click on "Settings". Click on "Delete Environment".
 
-<img src="07-using_platforms_modules_files/figure-html//182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_gf243efded1_0_140.png" alt="Screenshot of the cloud environment pop out menu. The “DELETE ENVIRONMENT OPTIONS” link is highlighted." width="100%" />
+<img src="07-using_platforms_modules_files/figure-html//1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q_ge20e585f11_0_256.png" alt="Screenshot of the cloud environment pop out menu. The &quot;Delete Environment&quot; button is highlighted." width="100%" />
 
-Finally, select “Delete everything, including persistent disk”. Make sure you are done with the activity and then click “DELETE”.
+Finally, select "Delete everything, including persistent disk". Make sure you are done with the activity and then click "Delete".
 
-<img src="07-using_platforms_modules_files/figure-html//182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_gf243efded1_0_146.png" 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%" />
+<img src="07-using_platforms_modules_files/figure-html//1UIfBMQcujMzyNTyIiMXQ6eU0DdWHmI9QUtseGylg6Ms_g117989bd49c_0_0.png" 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%" />
 ::::
 
 ## Video overview on using RStudio
@@ -304,6 +313,22 @@ Next, we will be using RStudio and the package `Glimma` to create interactive pl
 
 :::: {.borrowed_chunk}
 
+1. You can view costs and make changes to your cloud environments from the panel on the far right of the page.  If you don’t see this panel, you may need to scroll to the right.  Running environments will have a green dot, and paused environments will have an orange dot.
+
+    <img src="07-using_platforms_modules_files/figure-html//16s-TjOg19RrkxS9sM9fGfD0M_WIxlw-e8PFWDymjvRU_g230ed3a46c7_0_0.png" alt="Screenshot of the RStudio interface. The cloud environment panel on the right is highlighted." width="100%" />
+
+1. Hovering over the RStudio icon will show you the costs associated with your RStudio environment.  Click on the RStudio icon to open the cloud environment settings.
+
+    <img src="07-using_platforms_modules_files/figure-html//16s-TjOg19RrkxS9sM9fGfD0M_WIxlw-e8PFWDymjvRU_g230ed3a46c7_0_6.png" alt="Screenshot of the cloud environment panel.  The RStudio icon is highlighted." width="100%" />
+
+1. Click the Pause button to pause RStudio.  This will take a few minutes.
+
+    <img src="07-using_platforms_modules_files/figure-html//16s-TjOg19RrkxS9sM9fGfD0M_WIxlw-e8PFWDymjvRU_g230ed3a46c7_0_231.png" alt="Screenshot of the RStudio cloud environment settings. The Pause button is highlighted." width="100%" />
+
+1. When the environment is paused, an orange dot will be displayed next to the RStudio icon.  If you hover over the icon, you will see that it is paused, and has a small ongoing cost as long as it is paused.  When you’re ready to resume working, you can do so by clicking the RStudio icon and clicking Resume.
+
+    <img src="07-using_platforms_modules_files/figure-html//16s-TjOg19RrkxS9sM9fGfD0M_WIxlw-e8PFWDymjvRU_g230ed3a46c7_0_237.png" alt="Screenshot of a Terra Workspace Dashboard. The RStudio icon in the far right panel is highlighted.  It has an orange dot next to it indicating the cloud environment is paused." width="100%" />
+
 1. 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.
 
     <img src="07-using_platforms_modules_files/figure-html//1BLTCaogA04bbeSD1tR1Wt-mVceQA6FHXa8FmFzIARrg_g11f12bc99af_0_84.png" alt="Screenshot of the RStudio interface. The icon on the right showing that the cloud environment is running is highlighted." width="100%" />

docs/08-student_modules.md

@@ -10,40 +10,35 @@ Modules aimed at students in a course or workshop.
 
 :::: {.borrowed_chunk}
 
-In order to run your analyses, you will use the [AnVIL cloud computing platform](https://anvilproject.org/), 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.
+In order to run your analyses, you will use the [AnVIL cloud computing platform](https://anvilproject.org/).  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.
 
 :::{.notice}
 **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](https://anvil.terra.bio/) to provide many computational tools useful for biological data analysis, such as [RStudio](https://www.rstudio.com/products/rstudio/), [Galaxy](https://usegalaxy.org/), and [Jupyter Notebooks](https://jupyter.org/).  Terra takes care of installing these tools on Google's computers, so that you can just start using them.
+- Behind the scenes, AnVIL relies on Google Cloud Platform to provide computing infrastructure.  Basically, AnVIL lets you "rent" computers through the internet. The analysis is run on the rented computer. AnVIL lets you see the results in your browser.
+- AnVIL uses [Terra](https://anvil.terra.bio/) to provide many computational tools useful for biological data analysis, such as [RStudio](https://www.rstudio.com/products/rstudio/), [Galaxy](https://usegalaxy.org/), and [Jupyter Notebooks](https://jupyter.org/).  Terra takes care of installing these tools so you can use them right away.
 :::
 
 ### 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](https://accounts.google.com/SignUp).
+A Google account usually looks like "`[email protected]`". Alternatively, you can enable Google for an existing non-Gmail email address using [these instructions](https://support.terra.bio/hc/en-us/articles/360029186611).
 
-- 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](https://support.terra.bio/hc/en-us/articles/360029186611).
+If you do not already have a Google account that you would like to use for accessing AnVIL, [create one now](https://accounts.google.com/SignUp).
 
 ### 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`](https://anvil.terra.bio/), or by clicking the link on the [AnVIL home page](https://anvilproject.org/).
-
-
-<img src="08-student_modules_files/figure-html//1-PVlDAzmDncjcCHIy9ZyR3ROyPpfjrg46LhEQopDc1Q_g22c9add987a_0_5.png" alt="Screenshot of the AnVIL home page. The section descring Terra is highlighted." width="100%" />
-
-Open Terra, and you should be prompted to sign in with your Google account.
+You can access Terra by going to [`anvil.terra.bio`](https://anvil.terra.bio/). Open Terra, and you should be prompted to sign in with your Google account.
 
 ### Share Username
 
-Finally, make sure your instructor has your Google account username (e.g. `[email protected]`), so they can give you access to everything you need.
+Make sure your instructor has your Google account username (e.g. `[email protected]`), 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
+- If you have multiple Google accounts, make sure you give them the username that you will be using to log in to `anvil.terra.bio`.
 
 :::{.warning}
 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.

docs/404.html

@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-08-23" />
+<meta name="date" content="2024-08-27" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -231,11 +231,7 @@
 </ul></li>
 <li class="chapter" data-level="7" data-path="using-programming-platforms-on-anvil.html"><a href="using-programming-platforms-on-anvil.html"><i class="fa fa-check"></i><b>7</b> Using programming platforms on AnVIL</a>
 <ul>
-<li class="chapter" data-level="7.1" data-path="using-programming-platforms-on-anvil.html"><a href="using-programming-platforms-on-anvil.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="using-programming-platforms-on-anvil.html"><a href="using-programming-platforms-on-anvil.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="using-programming-platforms-on-anvil.html"><a href="using-programming-platforms-on-anvil.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
-</ul></li>
+<li class="chapter" data-level="7.1" data-path="using-programming-platforms-on-anvil.html"><a href="using-programming-platforms-on-anvil.html#video-overview-on-using-jupyter-notebooks"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Jupyter Notebooks</a></li>
 <li class="chapter" data-level="7.2" data-path="using-programming-platforms-on-anvil.html"><a href="using-programming-platforms-on-anvil.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="using-programming-platforms-on-anvil.html"><a href="using-programming-platforms-on-anvil.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.3</b> Video overview on using Galaxy</a></li>
 <li class="chapter" data-level="7.4" data-path="using-programming-platforms-on-anvil.html"><a href="using-programming-platforms-on-anvil.html#starting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Starting Galaxy</a></li>

docs/About.md

@@ -53,7 +53,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-08-23
+##  date     2024-08-27
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────