6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f
mspeir
  Wed Jul 8 09:23:00 2026 -0700
redoing slides as embedded html slide deck, refs #37292

diff --git docs/browserSlideDecks.md docs/browserSlideDecks.md
index 4a49ff7f196..6bdb6708de8 100644
--- docs/browserSlideDecks.md
+++ docs/browserSlideDecks.md
@@ -1,33 +1,79 @@
 ---
 title: "UCSC Genome Browser Slide Decks"
 ---
 
 This page collects training slides for the UCSC Genome Browser. Each slide deck
-has been curated with a specific purpose, such as cancer data analysis.
-Feel free to download these and use them in your courses or local trainings.
+has been curated with a specific purpose, from basic navigation to interpreting
+clinical variants. They are self-contained web decks: open one in any browser,
+present it full-screen (press <kbd>F</kbd>), read the presenter notes
+(press <kbd>S</kbd>), or jump to any slide from its **Contents** page. Feel free
+to use them in your courses or local trainings.
 [Contact us](/contacts.html) to suggest new slide decks or improvements to the
 current ones.
 
-## Slide Deck 1: UCSC Genome Browser Basics
+## Deck 1: UCSC Genome Browser Basics
 
-This slide deck covers basic features and navigation of the
-[main genome browser display](/cgi-bin/hgTracks). This includes
-configuring tracks, uploading custom data, and aligning sequences with BLAT.
-[Download](https://docs.google.com/presentation/d/1yRAGCWx21KMFJophVfctcZETACFA3qgVkxkTbmVvA5U/edit?usp=sharing)
-these slides to present them or modify them for your own use.
+Basic features and navigation of the
+[main genome browser display](/cgi-bin/hgTracks): configuring tracks and display
+modes, reading the gene model, the track groups, viewing and extracting DNA, the
+Table Browser, aligning sequences with BLAT, and loading your own data as custom
+tracks, track hubs, and sessions.
+
+**[&#9654; Open the deck](/docs/slideDecks/tutorial1-basics/presentation/)**
+&nbsp;·&nbsp; [Contents](/docs/slideDecks/tutorial1-basics/tableOfContents/)
+
+<br>
+<iframe src="/docs/slideDecks/tutorial1-basics/presentation/" width="720" height="450" style="max-width:100%;border:1px solid #ccc;border-radius:6px;" frameborder="0" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true" title="Deck 1: UCSC Genome Browser Basics"></iframe>
+
+## Deck 2: Cancer Data in the Genome Browser
+
+An overview of the cancer and clinical databases hosted by the Genome Browser,
+organized by **somatic** and **germline** diagnosis and worked on the
+<em>BRAF</em> V600E example: CIViC, COSMIC, ClinVar, and TCGA Pan-Cancer for
+somatic variants, and GenCC, OMIM, and gnomAD for germline questions.
+
+**[&#9654; Open the deck](/docs/slideDecks/tutorial2-cancer/presentation/)**
+&nbsp;·&nbsp; [Contents](/docs/slideDecks/tutorial2-cancer/tableOfContents/)
 
 <br>
-<iframe src="https://docs.google.com/presentation/d/e/2PACX-1vQsrUr1DLp-KzcC9diMz-Mf7UDohlctbZKBZ0dPgHOX7bnTCw-5ag__PNQWf6Plp2_I2EipyzlpG4B7/pubembed?start=false&loop=false&delayms=60000" frameborder="0" width="480" height="299" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true" title="Slide Deck 1: UCSC Genome Browser Basics"></iframe>
+<iframe src="/docs/slideDecks/tutorial2-cancer/presentation/" width="720" height="450" style="max-width:100%;border:1px solid #ccc;border-radius:6px;" frameborder="0" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true" title="Deck 2: Cancer Data in the Genome Browser"></iframe>
 
-## Slide Deck 2: Cancer Data in the Genome Browser
+## Deck 3: Clinical Examples & Variant Interpretation
 
-This slide deck provides an overview of cancer data hosted by the UCSC Genome
-Browser (e.g. TCGA, OMIM, and GenCC) and how one might analyze cancer data
-using Genome Browser tools.
-[Download](https://docs.google.com/presentation/d/12agh_HbEriQADnhXM0LjbAxv5Oz7_W-qlS_vfXC0i14/edit?usp=sharing)
-these slides to present them or modify them for your own use.
+How to interpret a variant end to end: the **Recommended Track Sets**, the
+regulatory and epigenetic context that non-coding variants need, worked germline
+(<em>BRCA2</em>) and somatic (<em>BRAF</em> V600E) examples, expression, and AI
+predictors such as AlphaMissense and SpliceAI.
+
+**[&#9654; Open the deck](/docs/slideDecks/tutorial3-clinical/presentation/)**
+&nbsp;·&nbsp; [Contents](/docs/slideDecks/tutorial3-clinical/tableOfContents/)
 
 <br>
-<iframe src="https://docs.google.com/presentation/d/e/2PACX-1vSzR-IeJFHp6V6odCAxfaB0KxLyxzD4pqxKlOKMAikF25zjYI9LjqmfT5zmvc19qriH3Gholv047wQf/pubembed?start=false&loop=false&delayms=60000" frameborder="0" width="480" height="299" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true" title="Slide Deck 2: Cancer Data in the Genome Browser"></iframe>
+<iframe src="/docs/slideDecks/tutorial3-clinical/presentation/" width="720" height="450" style="max-width:100%;border:1px solid #ccc;border-radius:6px;" frameborder="0" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true" title="Deck 3: Clinical Examples and Variant Interpretation"></iframe>
+
+## Deck 4: Clinical Case Studies
 
+A set of real diagnostic cases spanning variant classes, each opening as a live
+Genome Browser session: coding variants, splicing (deep-intronic and synonymous),
+non-coding and regulatory variants, structural variants (CNVs), and repeat
+expansions.
 
+**[&#9654; Open the deck](/docs/slideDecks/tutorial4-clinical-cases/presentation/)**
+&nbsp;·&nbsp; [Contents](/docs/slideDecks/tutorial4-clinical-cases/tableOfContents/)
+
+<br>
+<iframe src="/docs/slideDecks/tutorial4-clinical-cases/presentation/" width="720" height="450" style="max-width:100%;border:1px solid #ccc;border-radius:6px;" frameborder="0" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true" title="Deck 4: Clinical Case Studies"></iframe>
+
+## Deck 5: Teaching with the Browser
+
+Ready-made, interactive teaching modules from our
+[Education portal](/training/education/): the central dogma (reading frames,
+codons, splicing), variant effects (synonymous, missense, nonsense, frameshift),
+and real disease and evolution case studies. Each module is a clickable session
+plus a short page, ready to drop into a lecture or assignment.
+
+**[&#9654; Open the deck](/docs/slideDecks/tutorial5-teaching/presentation/)**
+&nbsp;·&nbsp; [Contents](/docs/slideDecks/tutorial5-teaching/tableOfContents/)
+
+<br>
+<iframe src="/docs/slideDecks/tutorial5-teaching/presentation/" width="720" height="450" style="max-width:100%;border:1px solid #ccc;border-radius:6px;" frameborder="0" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true" title="Deck 5: Teaching with the Browser"></iframe>