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. + +**[▶ 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. + +**[▶ Open the deck](/docs/slideDecks/tutorial2-cancer/presentation/)** + · [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. + +**[▶ Open the deck](/docs/slideDecks/tutorial3-clinical/presentation/)** + · [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. +**[▶ 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. + +**[▶ 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>