diff --git a/.github/workflows/delete-preview.yml b/.github/workflows/delete-preview.yml
index 88dc705..faa83cc 100644
--- a/.github/workflows/delete-preview.yml
+++ b/.github/workflows/delete-preview.yml
@@ -18,7 +18,7 @@ jobs:
 
       # Check out current repository
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 6bebd6b..c58b39a 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -1,4 +1,5 @@
-# Candace Savonen Aug 2022
+# Candace Savonen 2021
+# Updated Jan 2023
 
 name: Pull Request
 
@@ -13,9 +14,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          token: ${{ secrets.GH_PAT }}
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -23,14 +25,6 @@ jobs:
         with:
             files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
 
-      - name: Verify Dockerfiles changed?
-        uses: tj-actions/verify-changed-files@v8.8
-        id: verify-changed-files
-        with:
-          files: |
-             docker/Dockerfile
-             docker/github_package_list.tsv
-
       # Delete the branch if this has been run before
       - name: Delete branch locally and remotely
         run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
@@ -38,8 +32,9 @@ jobs:
       # Make the branch fresh
       - name: Make the branch fresh
         run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
 
           branch_name='preview-${{ github.event.pull_request.number }}'
           echo branch doesnt exist
@@ -47,15 +42,14 @@ jobs:
           git push --set-upstream origin $branch_name
         shell: bash
 
+
     outputs:
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
       toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
-      toggle_docker_build: "${{ env.DOCKER_BUILD }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
-      dockerfiles_changed: steps.verify-changed-files.outputs.files_changed
 
 ########################## Make the error reports ##############################
   spell-check:
@@ -67,6 +61,7 @@ jobs:
       check_type: spelling
       error_min: 3
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   url-check:
     name: Check URLs
@@ -77,6 +72,7 @@ jobs:
       check_type: urls
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   quiz-check:
     name: Check quiz formatting
@@ -87,6 +83,7 @@ jobs:
       check_type: quiz_format
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
 ############################# Style the code ###################################
   style-code:
@@ -99,7 +96,7 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -108,6 +105,7 @@ jobs:
 
       - name: Commit styled files
         run: |
+          git config --system --add safe.directory "$GITHUB_WORKSPACE"
           git add \*.Rmd
           git commit -m 'Style Rmds' || echo "No changes to commit"
           git push origin || echo "No changes to commit"
@@ -124,15 +122,16 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       # Set up git checkout
       - name: Set up git checkout
         run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
 
           branch_name='preview-${{ github.event.pull_request.number }}'
           git fetch --all
@@ -167,7 +166,7 @@ jobs:
         run: |
           branch_name='preview-${{ github.event.pull_request.number }}'
           git diff origin/main -- docs >/dev/null && changes=true || changes=false
-          echo ::set-output name=changes::$changes
+          echo "changes=$changes" >> $GITHUB_OUTPUT
           git add . --force
           git commit -m 'Render preview' || echo "No changes to commit"
           git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
@@ -175,7 +174,7 @@ jobs:
         shell: bash
 
       - name: Find Comment
-        uses: peter-evans/find-comment@v1
+        uses: peter-evans/find-comment@v2
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}
@@ -189,16 +188,16 @@ jobs:
           bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
           tocless_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
           docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/docs/$course_name.docx")
-          echo ::set-output name=bookdown_link::$bookdown_link
-          echo ::set-output name=tocless_link::$tocless_link
-          echo ::set-output name=docx_link::$docx_link
-          echo ::set-output name=time::$(date +'%Y-%m-%d')
-          echo ::set-output name=commit_id::$GITHUB_SHA
+          echo "bookdown_link=$bookdown_link" >> $GITHUB_OUTPUT
+          echo "tocless_link=$tocless_link" >> $GITHUB_OUTPUT
+          echo "docx_link=$docx_link" >> $GITHUB_OUTPUT
+          echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
+          echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
           echo ${{steps.commit.outputs.changes}}
 
       - name: Create or update comment
         if: steps.commit.outputs.changes == 'true'
-        uses: peter-evans/create-or-update-comment@v1
+        uses: peter-evans/create-or-update-comment@v2
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}
@@ -213,7 +212,7 @@ jobs:
 
       - name: Comment if no changes
         if: steps.commit.outputs.changes == 'false'
-        uses: peter-evans/create-or-update-comment@v1
+        uses: peter-evans/create-or-update-comment@v2
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}
@@ -222,56 +221,3 @@ jobs:
 
             _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
           edit-mode: replace
-
-############################## Build Docker ####################################
-
-  build-docker:
-    name: Build Docker image
-    needs: yaml-check
-    runs-on: ubuntu-latest
-    if: ${{needs.yaml-check.outputs.toggle_docker_build == 'yes' && needs.yaml-check.outputs.dockerfiles_changed == 'true' && github.head_ref != 'repo-sync/OTTR_Template/default'}}
-
-    steps:
-      - name: checkout repo
-        uses: actions/checkout@v2
-
-      - name: Verify Dockerfiles changed?
-        uses: tj-actions/verify-changed-files@v8.8
-        id: verify-changed-files
-        with:
-          files: |
-             docker/Dockerfile
-             docker/github_package_list.tsv
-
-      - name: Login as jhudsl-robot
-        run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
-
-      # Set up Docker build
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
-
-      # Setup layer cache
-      - name: Cache Docker layers
-        uses: actions/cache@v2
-        with:
-          path: /tmp/.buildx-cache
-          key: ${{ runner.os }}-buildx-${{ github.sha }}
-          restore-keys: |
-            ${{ runner.os }}-buildx-
-
-      - name: Set up Docker Build
-        uses: docker/setup-buildx-action@v1
-
-      - name: Get token
-        run: echo ${{ secrets.GH_PAT }} > docker/git_token.txt
-
-      - name: Build Docker image
-        uses: docker/build-push-action@v2
-        with:
-          push: false
-          load: true
-          context: docker
-          file: docker/Dockerfile
-          tags: jhudsl/base_ottr
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 407e1ca..7810e38 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -10,6 +10,7 @@ on:
     paths:
       - '**.Rmd'
       - assets/*
+      - quizzes/*
 
 jobs:
 
@@ -18,7 +19,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -29,6 +30,7 @@ jobs:
       toggle_bookdown: "${{ env.RENDER_BOOKDOWN }}"
       toggle_coursera: "${{ env.RENDER_COURSERA }}"
       toggle_leanpub: "${{ env.RENDER_LEANPUB }}"
+      make_book_txt: "${{ env.MAKE_BOOK_TXT }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
 
@@ -42,16 +44,16 @@ jobs:
 
     steps:
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
 
       - name: Login as jhudsl-robot
         run: |
-
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
 
       # We want a fresh run of the renders each time
       - name: Delete old docs/*
@@ -78,10 +80,11 @@ jobs:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
           git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
           git add --force docs/*
           git commit -m 'Render bookdown' || echo "No changes to commit"
           git pull --allow-unrelated-histories --strategy-option=ours
-          git push origin main || echo "No changes to push"
+          git push -u origin main  || echo "No changes to push"
 
   render-tocless:
     name: Render TOC-less version for Leanpub or Coursera
@@ -93,15 +96,16 @@ jobs:
 
     steps:
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
 
       - name: Login as jhudsl-robot
         run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
 
       # Rendered content for Leanpub and Coursera is very similar.
       # This job creates a shared scaffold for both.
@@ -115,10 +119,11 @@ jobs:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
           git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
           git add --force docs/no_toc*
           git commit -m 'Render toc-less' || echo "No changes to commit"
           git pull --allow-unrelated-histories --strategy-option=ours
-          git push origin main || echo "No changes to push"
+          git push -u origin main  || echo "No changes to push"
 
   render-leanpub:
     name: Finish Leanpub prep
@@ -130,15 +135,16 @@ jobs:
 
     steps:
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
 
       - name: Login as jhudsl-robot
         run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
 
       # Create screenshots
       - name: Run the screenshot creation
@@ -153,8 +159,17 @@ jobs:
             --output_dir resources/chapt_screen_images)
 
       # We want a fresh run of the renders each time
-      - name: Delete old manuscript/
-        run: rm -rf manuscript/
+      - name: Delete manuscript/
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+        run: |
+          rm -rf manuscript/
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git add .
+          git commit -m 'Delete manuscript folder' || echo "No changes to commit"
+          git pull --allow-unrelated-histories --strategy-option=ours
+          git push -u origin main || echo "No changes to push"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
         if: needs.yaml-check.outputs.toggle_quiz_check == 'no'
@@ -162,7 +177,7 @@ jobs:
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
             chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
-            make_book_txt = TRUE, \
+            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'), \
             quiz_dir = NULL)"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
@@ -171,20 +186,20 @@ jobs:
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
             chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
-            make_book_txt = TRUE)"
+            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'))"
 
       # Commit the rendered Leanpub files
       - name: Commit rendered Leanpub files
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
-          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          mkdir -p manuscript
           git add --force manuscript/*
           git add --force resources/*
           git add --force docs/*
           git commit -m 'Render Leanpub' || echo "No changes to commit"
           git pull --allow-unrelated-histories --strategy-option=ours
-          git push origin main || echo "No changes to push"
+          git push --force --set-upstream origin main || echo "No changes to push"
 
   render-coursera:
     name: Finish Coursera prep
@@ -196,15 +211,16 @@ jobs:
 
     steps:
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
 
       - name: Login as jhudsl-robot
         run: |
-          git config --local user.email "itcrtrainingnetwork@gmail.com"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.email "itcrtrainingnetwork@gmail.com"
+          git config --global user.name "jhudsl-robot"
 
       # Run Coursera version
       - name: Convert Leanpub quizzes to Coursera
@@ -218,9 +234,10 @@ jobs:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
           git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
           git add --force manuscript/*
           git add --force resources/*
           git add --force docs/*
           git commit -m 'Render Coursera quizzes' || echo "No changes to commit"
           git pull --allow-unrelated-histories --strategy-option=ours
-          git push origin main || echo "No changes to push"
+          git push -u origin main  || echo "No changes to push"
diff --git a/.github/workflows/transfer-rendered-files.yml b/.github/workflows/transfer-rendered-files.yml
index df91b77..e698d98 100644
--- a/.github/workflows/transfer-rendered-files.yml
+++ b/.github/workflows/transfer-rendered-files.yml
@@ -21,7 +21,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -60,12 +60,12 @@ jobs:
           results=$(Rscript --vanilla git_repo_check.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT")
           echo $QUIZ_REPO exists: $results
 
-          echo "::set-output name=git_results::$results"
-          echo "::set-output name=leanpub_repo::$QUIZ_REPO"
+          echo "git_results=$results" >> $GITHUB_OUTPUT
+          echo "leanpub_repo=$QUIZ_REPO" >> $GITHUB_OUTPUT
 
       - name: Checkout code from Leanpub repo
         if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           repository: ${{ steps.git_repo_check.outputs.leanpub_repo }}
           token: ${{ secrets.GH_PAT }}
@@ -79,9 +79,9 @@ jobs:
           # Copy over images folder
           svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/resources/chapt_screen_images resources/chapt_screen_images
 
-          # Copy over _bookdown.yml 
+          # Copy over _bookdown.yml
           svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/_bookdown.yml _bookdown.yml
-          
+
       - name: Create PR with resources files
         if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
         uses: peter-evans/create-pull-request@v3
diff --git a/03-version-control-with-github.Rmd b/03-version-control-with-github.Rmd
index 8540e11..442eaf0 100644
--- a/03-version-control-with-github.Rmd
+++ b/03-version-control-with-github.Rmd
@@ -33,7 +33,7 @@ GitKraken is nice because they have lots of nice tutorials, it works pretty well
 
 ### Install GitKraken
 
-[Go here to install GitKraken](https://support.gitkraken.com/how-to-install/).
+[Go here to install GitKraken](https://www.gitkraken.com/).
 
 Follow their instructions to sign in with your GitHub account. It will ask you to authorize your GitHub account to connect to GitKraken. Click `Authorize`.
 
@@ -77,7 +77,7 @@ mkdir -p chapter-zips
 wget -O chapter-zips/reproducible-python-example.zip https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/reproducible-python-example.zip
 ```
 
-Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc)).
+Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc).
 
 ```{bash, include = FALSE}
 unzip -o chapter-zips/reproducible-python-example.zip -d chapter-zips/
@@ -92,7 +92,7 @@ mkdir -p chapter-zips
 wget -O chapter-zips/reproducible-R-example.zip https://raw.githubusercontent.com/jhudsl/Reproducibility_in_Cancer_Informatics/main/chapter-zips/reproducible-R-example.zip
 ```
 
-Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc)).
+Now double click your chapter zip file to unzip. For Windows you may have to [follow these instructions](https://support.microsoft.com/en-us/windows/zip-and-unzip-files-f6dde0a7-0fec-8294-e1d3-703ed85e7ebc).
 
 ```{bash, include = FALSE}
 unzip -o chapter-zips/reproducible-R-example.zip -d chapter-zips/
@@ -246,7 +246,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1IJ_uFxJud7OdIAr6
 
 ## More resources for learning GitHub
 
-- [Happy Git and GitHub for the useR](https://happygitwithr.com/) by @Bryan2021.
+- [Happy Git and GitHub for the useR](https://happygitwithr.com) by @Bryan2021.
 - [GitHub for data scientists](https://towardsdatascience.com/introduction-to-github-for-data-scientists-2cf8b9b25fba) by @Vickery2019.
 - [Intro to GitHub](https://github.com/skills/introduction-to-github) by @GitHub2022.
 - [First Day on GitHub](https://skills.github.com/#first-day-on-github) by @GitHub2022c.
diff --git a/04-data-handling.Rmd b/04-data-handling.Rmd
index ee11539..1747944 100644
--- a/04-data-handling.Rmd
+++ b/04-data-handling.Rmd
@@ -38,7 +38,7 @@ wget -h
 wget -O <FOLDER/FILE_TO_SAVE_TO> <URL>
 ```
 
-You can download this [general template download file here](https://raw.githubusercontent.com/AlexsLemonade/training-specific-template/main/working-with-your-data/template-scripts/wget-TEMPLATE.sh) [@Shapiro2021].
+You can download this [general template download file here](https://raw.githubusercontent.com/AlexsLemonade/training-specific-template/main/additional-resources/template-scripts/wget-TEMPLATE.sh) [@Shapiro2021].
 
 ### Examples of data download scripts
 
@@ -46,4 +46,4 @@ You can download this [general template download file here](https://raw.githubus
 - [Data download script for multiple files of the same place](https://github.com/AlexsLemonade/training-modules/blob/master/machine-learning/setup/00-data-download.sh)
 - [Data download script - refine.bio example](https://github.com/jhudsl/reproducible-R-example/blob/main/00-download-data.py)
 
-For more about data sharing techniques, see the [Ethical Data Handling for Cancer Research](https://jhudatascience.org/Ethical_Data_Handling_for_Cancer_Research/) course</a>.
+For more about data sharing techniques, see the [Ethical Data Handling for Cancer Research](https://github.com/fhdsl/Ethical_Data_Handling_for_Cancer_Research) course</a>.
diff --git a/08-modifying-docker-image.Rmd b/08-modifying-docker-image.Rmd
index eb582f8..5455ed9 100644
--- a/08-modifying-docker-image.Rmd
+++ b/08-modifying-docker-image.Rmd
@@ -31,7 +31,7 @@ To see what images you have on your internet repository, you can log on to docke
 ottrpal::include_slide("https://docs.google.com/presentation/d/1IJ_uFxJud7OdIAr6p8ZOzvYs-SGDqa7g4cUHtUld03I/edit#slide=id.gfc8849fa4d_0_38")
 ```
 
-After you sign into dockerhub, you can see the list of repositories you have stored online. At this point, you won’t have any if you just created your dockerhub account. To create a new repository, click the ‘Create Repository’ button.
+After you sign into dockerhub, click on the `Repositories` tab, so you can see the list of repositories you have stored online. At this point, you won’t have any if you just created your dockerhub account. To create a new repository, click the ‘Create Repository’ button.
 
 ```{r, fig.alt="In your dockerhub main page, you can see the list of repositories you have stored online. At this point, you won’t have any if you just created your dockerhub account. To create a new repository, click the ‘Create Repository’ button.", out.width = "100%", echo = FALSE}
 ottrpal::include_slide("https://docs.google.com/presentation/d/1IJ_uFxJud7OdIAr6p8ZOzvYs-SGDqa7g4cUHtUld03I/edit#slide=id.gfc8849fa4d_0_10")
@@ -52,7 +52,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1IJ_uFxJud7OdIAr6
 
 Go to your [local command line](https://towardsdatascience.com/a-quick-guide-to-using-command-line-terminal-96815b97b955) and use the command specified on the right side of your repository page. You don't have to specify a tagname if you don't want to.  If you don't want to specify a tagname, leave off the `:tagname` if you like.
 
-Now you will be able to test pulling your image using `docker pull <image name>` like we did in the previous chapter.
+Now you will be able to test pulling your image using `docker pull <image name>` like we did in the previous chapter. You can also click on the `Public View` button to copy the pull command for your Docker image.
 
 Docker images can be pulled from being stored online but these images are built originally from a `Dockerfile`.
 
@@ -143,7 +143,7 @@ If all built successfully, you should see a message like:
 => => naming to docker.io/library/image_name
 ```
 
-Now to run the image we can use the docker run command we used in the previous chapter and we should have a message: `Yay! I added to this Docker image` pop up upon building.
+Now to run the image we can use the docker run command we used in the previous chapter (see below) and we should have a message: `Yay! I added to this Docker image` pop up upon building.
 
 <details> <summary> To run your new **Python docker image** </summary>
 But replace `image_name` with whatever you have called your image.
diff --git a/assets/box_images/under_construction.png b/assets/box_images/under_construction.png
new file mode 100644
index 0000000..a67bd5c
Binary files /dev/null and b/assets/box_images/under_construction.png differ
diff --git a/resources/exclude_files.txt b/resources/exclude_files.txt
new file mode 100644
index 0000000..0e6200f
--- /dev/null
+++ b/resources/exclude_files.txt
@@ -0,0 +1,7 @@
+About.Rmd
+docs/*
+style-sets/*
+manuscript/*
+LICENSE.md
+README.md
+code_of_conduct.md
diff --git a/style-sets/fhdasl/_output.yml b/style-sets/fhdasl/_output.yml
index 353e612..d00716f 100644
--- a/style-sets/fhdasl/_output.yml
+++ b/style-sets/fhdasl/_output.yml
@@ -3,14 +3,15 @@ bookdown::gitbook:
   includes:
     before_body: assets/big-image_fhdasl.html
     after_body: assets/footer.html
+  split_bib: false
   highlight: tango
   config:
     toc:
       collapse: section
       before: |
-       <a href="https://hutchdatascience.org/" target="_blank"><img src="assets/FHDaSL_SQ-funfetti.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
+       <a href="https://hutchdatascience.org/" target="_blank"><img src="assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
       after: |
        <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="http://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
-       <a href="http://hutchdatascience.org/"><img src="https://hutchdatascience.org/images/FHDataScienceLab_Rec_funfetti.png" style=" width: 80%; padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
+       <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
        <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
+       <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span>  <a href="https://forms.gle/W6Mg4rzuMK6Yk3Am8"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
diff --git a/style-sets/fhdasl/copy_to_assets/big-dasl-stacked.png b/style-sets/fhdasl/copy_to_assets/big-dasl-stacked.png
new file mode 100644
index 0000000..4bf74fc
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diff --git a/style-sets/fhdasl/copy_to_assets/big-dasl.png b/style-sets/fhdasl/copy_to_assets/big-dasl.png
new file mode 100755
index 0000000..df1b20b
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/big-dasl.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/big-image.html b/style-sets/fhdasl/copy_to_assets/big-image.html
new file mode 100755
index 0000000..1df3779
--- /dev/null
+++ b/style-sets/fhdasl/copy_to_assets/big-image.html
@@ -0,0 +1,12 @@
+<head>
+  <meta name="viewport" content="width=device-width,minimum-scale=1.0,maximum-scale=1.0,initial-scale=1.0">
+  <!--script src="https://kit.fontawesome.com/6a26f47516.js"></script-->
+  <!--<script src="assets/hideOutput.js"></script>-->
+  <link href="assets/style.css" rel="stylesheet">
+</head>
+
+
+
+<div class="hero-image-container">
+  <img class= "hero-image" src= "https://github.com/jhudsl/OTTR_Template/raw/main/assets/dasl_thin_main_image.png">
+</div>
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/data.png b/style-sets/fhdasl/copy_to_assets/box_images/data.png
new file mode 100644
index 0000000..8725b99
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/data.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/dictionary.png b/style-sets/fhdasl/copy_to_assets/box_images/dictionary.png
new file mode 100644
index 0000000..75ddac7
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/dictionary.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/github.png b/style-sets/fhdasl/copy_to_assets/box_images/github.png
new file mode 100644
index 0000000..a93acd3
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/github.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/justice.png b/style-sets/fhdasl/copy_to_assets/box_images/justice.png
new file mode 100644
index 0000000..7780e05
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/justice.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/money.png b/style-sets/fhdasl/copy_to_assets/box_images/money.png
new file mode 100644
index 0000000..5b1b7e9
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/money.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/motivations.png b/style-sets/fhdasl/copy_to_assets/box_images/motivations.png
new file mode 100644
index 0000000..6a3242a
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/motivations.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/note.png b/style-sets/fhdasl/copy_to_assets/box_images/note.png
new file mode 100644
index 0000000..72de3ae
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diff --git a/style-sets/fhdasl/copy_to_assets/box_images/plan.png b/style-sets/fhdasl/copy_to_assets/box_images/plan.png
new file mode 100644
index 0000000..24f4213
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/plan.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/question.png b/style-sets/fhdasl/copy_to_assets/box_images/question.png
new file mode 100644
index 0000000..19ad5be
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diff --git a/style-sets/fhdasl/copy_to_assets/box_images/question_box.png b/style-sets/fhdasl/copy_to_assets/box_images/question_box.png
new file mode 100644
index 0000000..458281c
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/question_box.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/submit.png b/style-sets/fhdasl/copy_to_assets/box_images/submit.png
new file mode 100644
index 0000000..8a343c3
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/submit.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/thinking_face.png b/style-sets/fhdasl/copy_to_assets/box_images/thinking_face.png
new file mode 100644
index 0000000..c2c279a
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/thinking_face.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/box_images/warning.png b/style-sets/fhdasl/copy_to_assets/box_images/warning.png
new file mode 100644
index 0000000..405fb61
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/box_images/warning.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/brothers.png b/style-sets/fhdasl/copy_to_assets/brothers.png
new file mode 100644
index 0000000..93c565e
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/brothers.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/dasl_thin_main_image.png b/style-sets/fhdasl/copy_to_assets/dasl_thin_main_image.png
index f1e5c99..6143f4f 100644
Binary files a/style-sets/fhdasl/copy_to_assets/dasl_thin_main_image.png and b/style-sets/fhdasl/copy_to_assets/dasl_thin_main_image.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/favicon.ico b/style-sets/fhdasl/copy_to_assets/favicon.ico
index 896b6d3..f41ff9b 100644
Binary files a/style-sets/fhdasl/copy_to_assets/favicon.ico and b/style-sets/fhdasl/copy_to_assets/favicon.ico differ
diff --git a/style-sets/fhdasl/copy_to_assets/footer.html b/style-sets/fhdasl/copy_to_assets/footer.html
old mode 100644
new mode 100755
index 0b268e7..61e2071
--- a/style-sets/fhdasl/copy_to_assets/footer.html
+++ b/style-sets/fhdasl/copy_to_assets/footer.html
@@ -4,5 +4,6 @@
       All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
       <br>
       All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
+      <a href="https://hutchdatascience.org/" target="_blank"><img src="https://hutchdatascience.org/images/crazy-idea-wide.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
   </div>
 </center>
\ No newline at end of file
diff --git a/style-sets/fhdasl/copy_to_assets/hideOutput.js b/style-sets/fhdasl/copy_to_assets/hideOutput.js
new file mode 100755
index 0000000..245d55f
--- /dev/null
+++ b/style-sets/fhdasl/copy_to_assets/hideOutput.js
@@ -0,0 +1,57 @@
+/*$(document).ready(function() {
+  
+  
+  // Copy Button
+  $chunks = $('pre.sourceCode > code.sourceCode');
+  $chunks.each(function(i, val) {
+    $(this).prepend("<button class=\"button copy\"><i class=\"fa fa-copy fa-2x\"></i></button>").click(function() {
+      var $temp = $("<textarea>");
+      $("body").append($temp);
+      var content = $(this).clone().children("button").remove().end().text();
+      $temp.val(content).select();
+      document.execCommand("copy");
+      $temp.remove();
+    });
+  });
+  
+  
+  // Section anchors
+  $('.section h1, .section h2, .section h3, .section h4, .section h5').each(function() {
+    anchor = '#' + $(this).parent().attr('id');
+    $(this).addClass("hasAnchor").prepend('<a href="' + anchor + '" class="anchor"></a>');
+  });
+});*/
+  
+
+
+/* New Clipboard copy 
+function changeTooltipMessage(element, msg) {
+  var tooltipOriginalTitle=element.getAttribute('data-original-title');
+  element.setAttribute('data-original-title', msg);
+  $(element).tooltip('show');
+  element.setAttribute('data-original-title', tooltipOriginalTitle);
+}
+if(ClipboardJS.isSupported()) {
+  $(document).ready(function() {
+    var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>";
+    $("div.sourceCode").addClass("hasCopyButton");
+    // Insert copy buttons:
+    $(copyButton).prependTo(".hasCopyButton");
+    // Initialize tooltips:
+    $('.btn-copy-ex').tooltip({container: 'body'});
+    // Initialize clipboard:
+    var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', {
+      text: function(trigger) {
+        return trigger.parentNode.textContent;
+      }
+    });
+    clipboardBtnCopies.on('success', function(e) {
+      changeTooltipMessage(e.trigger, 'Copied!');
+      e.clearSelection();
+    });
+    clipboardBtnCopies.on('error', function() {
+      changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+    });
+  });
+}
+*/
\ No newline at end of file
diff --git a/style-sets/fhdasl/copy_to_assets/itcr_arrow.png b/style-sets/fhdasl/copy_to_assets/itcr_arrow.png
new file mode 100755
index 0000000..3f86cb2
Binary files /dev/null and b/style-sets/fhdasl/copy_to_assets/itcr_arrow.png differ
diff --git a/style-sets/fhdasl/copy_to_assets/style.css b/style-sets/fhdasl/copy_to_assets/style.css
index 1fee320..a56a195 100644
--- a/style-sets/fhdasl/copy_to_assets/style.css
+++ b/style-sets/fhdasl/copy_to_assets/style.css
@@ -1,4 +1,4 @@
-@import url('https://fonts.googleapis.com/css?family=Abril+Fatface|Karla:400,400i,700,700i|Lora:400,400i,700,700i&display=swap');
+@import url('https://fonts.googleapis.com/css?family=Abril+Fatface|Arimo:400,400i,700,700i|Tinos:400,400i,700,700i&display=swap');
 
 p.caption {
   color: #777;
@@ -50,11 +50,11 @@ pre code {
 /*------------- Body and header text---------------- */
 
 .book.font-family-1 {
-  font-family: 'Karla', arial, sans-serif;
+  font-family: Arial, 'Arimo', sans-serif;
 }
 
 h1, h2, h3, h4 {
-  font-family: 'Lora', arial, sans-serif;
+  font-family: 'Times New Roman', 'Tinos', serif;
 }
 
 
@@ -69,7 +69,7 @@ h1, h2, h3, h4 {
 }
 
 .title {
-  font-family: 'Lora';
+  font-family: 'Times New Roman', 'Tinos', serif;
   font-size: 4em !important;
   color: #1B365D;
   margin-top: 0.275em !important;
@@ -77,7 +77,7 @@ h1, h2, h3, h4 {
 }
 
 .subtitle {
-  font-family: 'Lora';
+  font-family: 'Times New Roman', 'Tinos', serif;
   color: #1B365D;
 }
 
@@ -142,7 +142,7 @@ color: #1B365D
 }
 
 .summary{
-  font-family: 'Karla', sans-serif;
+  font-family: Arial, 'Arimo', sans-serif;
 }
 
 /* all TOC list items, basically */
@@ -166,6 +166,24 @@ color: #1B365D
   padding-left: 11px !important;
 }
 
+.trapezoid {
+  width: 132px;
+  text-align: center;
+  position: relative;
+    left: 10px;
+  border-right: 50px solid #ffb809;
+  border-bottom: 50px solid #dbdbdb;
+  border-left: 50px solid #b842ca;
+  box-sizing: content-box;
+}
+.trapezoid span {
+  position: absolute;
+  top: 8px;
+  bottom: 5px;
+  left: 5%;
+  color: #dbdbdb;
+}
+
 
 li.appendix span, li.part span { /* for TOC part names */
   margin-top: 1em;
@@ -246,12 +264,18 @@ li.appendix span, li.part span { /* for TOC part names */
   width: 50%;
 }
 
+.click_to_expand_block {
+    padding: 1em;
+    padding-top: .5em;
+    border: 1px grey;
+    background: #E8E8E8;
+    color: black;
+}
 
 /* Sidebar formating --------------------------------------------*/
 /* from r-pkgs.org*/
 
-div.notice, div.warning, div.github, div.dictionary, div.reflection {
-  border-style: solid;
+div.notice, div.warning, div.github, div.dictionary, div.reflection, div.question, div.ethics{
   padding: 1em;
   margin: 1em 0;
   padding-left: 100px;
@@ -259,46 +283,162 @@ div.notice, div.warning, div.github, div.dictionary, div.reflection {
   background-repeat: no-repeat;
 }
 
-div.notice{
+ div.motivations, div.question_box, div.data, div.money, div.plan, div.submit{
+  padding: 1em;
+  padding-left: 100px;
+  min-height: 55px;
+  background-repeat: no-repeat;
+}
+
+div.motivations{
+  background-size: 70px;
+  background-position: 15px center;
+  background-repeat: no-repeat;
+  background-image: url("../assets/box_images/motivations.png");
+  display:flex;
+  align-items:center;
+}
+
+div.question_box{
+  background-size: 70px;
+  background-position: 15px center;
+  background-repeat: no-repeat;
+  background-image: url("../assets/box_images/question_box.png");
+  display:flex;
+  align-items:center;
+}
+
+div.data{
+  background-size: 70px;
+  background-position: 15px center;
+  background-repeat: no-repeat;
+  background-image: url("../assets/box_images/data.png");
+  display:flex;
+  align-items:center;
+}
+
+div.money{
+  background-size: 70px;
+  background-position: 15px center;
+  background-repeat: no-repeat;
+  background-image: url("../assets/box_images/money.png");
+  display:flex;
+  align-items:center;
+}
+
+div.plan{
+  background-size: 70px;
+  background-position: 15px center;
+  background-repeat: no-repeat;
+  background-image: url("../assets/box_images/plan.png");
+  display:flex;
+  align-items:center;
+}
+
+div.submit{
+  background-size: 70px;
+  background-position: 15px center;
+  background-repeat: no-repeat;
+  background-image: url("../assets/box_images/submit.png");
+  display:flex;
+  align-items:center;
+}
+
+div.question{
+  background-size: 70px;
+  background-position: 15px center;
+  background-color: #e8ebee;
+  background-repeat: no-repeat;
+  background-image: url("../assets/box_images/question.png");
+  display:flex;
+  align-items:center;
   border: 4px #00C1D5;
+  border-style: solid;
+  font-size: 20px;
+  font-weight: bold;
+}
+
+div.ethics{
+  background-size: 70px;
+  background-position: 15px center;
+  background-color: #e8ebee;
+  background-image: url("../assets/box_images/justice.png");
+  border: 4px #b842ca;
+  border-style: solid;
+}
+
+
+div.notice{
   background-size: 70px;
   background-position: 15px center;
   background-color: #e8ebee;
   background-image: url("../assets/box_images/note.png");
+  border: 4px #00C1D5;
+  border-style: solid;
 }
 
 div.warning{
-  border: 4px #e0471c;
   background-size: 70px;
   background-position: 15px center;
   background-color: #e8ebee;
   background-image: url("../assets/box_images/warning.png");
+  border: 4px #e0471c;
+  border-style: solid;
 }
 
 div.github{
-  border: 4px #000000;
+
   background-size: 70px;
   background-position: 15px center;
   background-color: #e8ebee;
   background-image: url("../assets/box_images/github.png");
+  border: 4px #000000;
+  border-style: solid;
 }
 
+
 div.dictionary{
-  border: 4px #00C1D5;
   background-size: 70px;
   background-position: 15px center;
   background-color: #e8ebee;
   background-image: url("../assets/box_images/dictionary.png");
+  border: 4px black;
+  border-style: solid;
 }
 
+
+div.dictionary_long{
+  padding: 1em;
+  padding-top: 20px;
+  padding-left: 100px;
+  min-height: 180px;
+  background-size: 70px;
+  background-color: #e8ebee;
+  background-image: url("../assets/box_images/dictionary.png");
+  background-repeat: no-repeat;
+  background-position: top 70px left 20px;
+  border: 4px black;
+  border-style: solid;
+}
 div.reflection{
-  border: 4px #00C1D5;
   background-size: 90px;
   background-position: 15px center;
   background-color: #e8ebee;
   background-image: url("../assets/box_images/thinking_face.png");
+  border: 4px #00C1D5;
+  border-style: solid;
 }
 
+div.blackbox{
+  padding: 1em;
+  margin: 1em 0;
+  min-height: 120px;
+  border: 4px #000000;
+  border-style: solid;
+  outline: 5px solid #ffb808;
+}
+
+
 /* .book .book-body .page-wrapper .page-inner section.normal is needed
    to override the styles produced by gitbook, which are ridiculously
    overspecified. Goal of the selectors is to ensure internal "margins"
@@ -418,7 +558,7 @@ a.anchor:hover {
 /* Footer */
 
 .footer {
-  font-family: "Lora", serif;
+  font-family: 'Times New Roman', 'Tinos', serif;
   font-size: .85em;
   color: #193a5c;
 }
diff --git a/style-sets/fhdasl/copy_to_assets/toc_close.css b/style-sets/fhdasl/copy_to_assets/toc_close.css
new file mode 100755
index 0000000..1bc6dab
--- /dev/null
+++ b/style-sets/fhdasl/copy_to_assets/toc_close.css
@@ -0,0 +1,21 @@
+/*Get rid of TOC stuff from https://github.com/rstudio/bookdown/issues/1251 */
+
+.book .book-body .page-wrapper .page-inner {
+  max-width: 100% !important;
+}
+
+.book.with-summary .book-header.fixed {
+    left: 0% !important;
+}
+
+.book.with-summary .book-body {
+    left: 0% !important;
+}
+
+.book.with-summary .book-summary {
+    width: 0% !important;
+}
+
+.book-body.fixed > div > .book-header.fixed > a:nth-child(1) {
+  visibility: hidden;
+}