603a734862321da4d9bde067c47a4a13175acc02 mspeir Thu Jul 23 09:24:22 2026 -0700 Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904 diff --git docs/browserSlideDecks.md docs/browserSlideDecks.md index 6bdb6708de8..b06031c4b94 100644 --- docs/browserSlideDecks.md +++ docs/browserSlideDecks.md @@ -1,79 +1,80 @@ --- 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, 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. +(press <kbd>S</kbd>, which opens them in a separate browser tab; close that tab +when you are done with them), 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. ## Deck 1: UCSC Genome Browser Basics 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. +modes, reading the gene model, browsing the track groups, viewing and extracting +DNA, querying the Table Browser, aligning sequences with BLAT, and loading your +own data as custom tracks, track hubs, and sessions. **[▶ Open the deck](/docs/slideDecks/tutorial1-basics/presentation/)** · [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. +organized by **somatic** and **germline** diagnosis CIViC, COSMIC, ClinVar, and TCGA +Pan-Cancer for somatic variants, and GenCC, OMIM, and gnomAD for germline +questions. These databases are explored with a consistent <em>BRAF</em> V600E example throughout. **[▶ Open the deck](/docs/slideDecks/tutorial2-cancer/presentation/)** · [Contents](/docs/slideDecks/tutorial2-cancer/tableOfContents/) <br> <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> ## Deck 3: Clinical Examples & Variant Interpretation 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. **[▶ Open the deck](/docs/slideDecks/tutorial3-clinical/presentation/)** · [Contents](/docs/slideDecks/tutorial3-clinical/tableOfContents/) <br> <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. **[▶ Open the deck](/docs/slideDecks/tutorial4-clinical-cases/presentation/)** · [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. +plus a short description of that session and what it shows, ready to drop into a lecture or assignment. **[▶ Open the deck](/docs/slideDecks/tutorial5-teaching/presentation/)** · [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>