61438453e9f8be7a5949725a688ac6cf709add28 lrnassar Tue Apr 28 13:06:10 2026 -0700 Restructure /docs/ landing page for new users; add docs-page styling. refs #36894 docs/index.md: rewrite as a beginner-first landing page. Replace the prior five-section structure with a flat five-H2 outline -- Tutorials, Visualize your own data, Share your work, Download data, Get help -- so every entry in the sidebar TOC maps to specific content rather than to a vague grouping. Promote the tutorial table from a buried H3 to top-level content. Drop sections that don't serve new users (the "Understanding assemblies/annotations" primer, the MySQL bullet, the mirror paragraph, the Multi-Region View specific mention, and the four scattered "Relevant FAQs" lists). Consolidate help into a single closer with contact, FAQ, workshops, and the suggestion form. Distinguish custom tracks vs track hubs ("simpler option" vs "more powerful and configurable"). Make tutorial titles the table links and drop the redundant Link column. docs/staticPage.lua: add a docs-page class to the row wrapper so /docs/- only CSS can be scoped without affecting other gbsPage static pages. src/hg/htdocs/staticStyle/gbStatic.css: add scoped .docs-page styles for the sidebar TOC ("On this page" label) and tables (roomier padding, zebra striping using the existing tr.even/tr.odd classes, subtle hover). All new rules are namespaced under .docs-page so the rest of the site is untouched. diff --git docs/index.md docs/index.md index b5f0647fb13..a849d76c7a9 100644 --- docs/index.md +++ docs/index.md @@ -1,125 +1,75 @@ --- title: "Genome Browser Documentation" --- -New to the Genome Browser? Start with our [Genome Browser Basics -tutorial](/docs/tutorials/gb101.html), a 15-minute walkthrough of the -interface, navigation, and track display. You can also browse our -[glossary](/docs/genomeBrowserGlossary.html) to learn common terms used throughout -this documentation. - -## Using the Genome Browser interface and tools - -The Genome Browser offers a dynamic interface for visualizing genomic data on -a variety of genome assemblies. In addition to visualization, there are several tools -for extracting data from the current visualization. - -### Tutorials -We offer detailed step-by-step tutorials for several of our tools: - -| Title | Description | Link | -| - | - | - | -| Genome Browser Basics | Learn the basics of the Genome Browser interface | [View tutorial](/docs/tutorials/gb101.html) | -| Gateway Page | Find and switch between genome assemblies | [View tutorial](/docs/tutorials/gatewayTutorial.html) | -| Table Browser | Query and download Genome Browser data | [View tutorial](/docs/tutorials/tableBrowserTutorial.html) | -| Custom Tracks | Display your own annotations on the Genome Browser | [View tutorial](/docs/tutorials/customTrackTutorial.html) | - -Navigate to our [Tutorial index](/docs/tutorials/index.html) to see them all. - -### Video tutorials -Our [training page](/training/index.html) has short how-to videos covering common -tasks like saving sessions, using BLAT and isPCR, finding SNPs in a gene, and -using Multi-Region View. We also offer in-person and virtual workshops, -[contact us](/contacts.html) to host one at your institution. - -## Understanding Genome Browser assemblies and annotations - -The Genome Browser allows for the visualization of annotations on -a variety of genome assemblies. A genome assembly is a reconstruction of -an organism's complete DNA sequence from shorter sequenced fragments. Different -assemblies of the same species may exist as sequencing technology improves -(e.g., hg19 vs. hg38 for human). - -- Use our [gateway page](/cgi-bin/hgGateway) to access popular assemblies or - search for an assembly of interest. Learn more from our - [tutorial](/docs/tutorials/gatewayTutorial.html). -- If your assembly is not available, [request it](/assemblySearch.html). - -The Genome Browser displays annotations as horizontal "tracks" layered beneath -the genome coordinate ruler. These tracks fall into several major categories: - -- Genes and Gene Predictions: curated and predicted gene models (GENCODE, - RefSeq, Augustus) -- Regulation: transcription factor binding, histone marks, DNase - hypersensitivity (ENCODE, Roadmap Epigenomics) -- Comparative Genomics: cross-species conservation scores, alignments (PhyloP, - PhastCons, chain/net) -- Variation: SNPs, structural variants, clinical variants (dbSNP, ClinVar, - gnomAD) -- Repeats: repetitive elements (RepeatMasker, Simple Repeats) -- Mapping and Sequencing: assembly structure, gaps, chromosome bands - -Each track has its own description page (accessible by clicking the track name) -with details on the data source, methods, and display conventions. Human and mouse -assemblies (e.g. hg38, hg19, mm10, or mm39) will include tracks across nearly -all of these categories. However, most assemblies may only have a basic set of -annotations (genes, repeats, assembly mapping). - -Relevant FAQs: - -- [Gene Tracks](/FAQ/FAQgenes.html) -- [Genome Browser Tracks](/FAQ/FAQtracks.html) - - -## Visualizing your own data - -The Genome Browser allows you to visualize your own data alongside the data we host: - -- [Custom tracks](/cgi-bin/hgCustom) - - See our [documentation](/goldenPath/help/customTrack.html) to learn how to load your own -- [Track hubs](/cgi-bin/hgHubConnect#unlistedHubs) - - See our [Hub Basics](/docs/hubs/hubBasics.html) page to learn how to build your own - - Validate your hub with our [hub development tools](/cgi-bin/hgHubConnect#hubDeveloper) - -For both hubs and custom tracks, we provide storage through [hub space](/cgi-bin/hgHubConnect#hubUpload). - -## Sharing your data - -Once you've loaded and configured your data, you can share it with others -through several means: - -- [Links](/FAQ/FAQlink.html) -- [Sessions](/cgi-bin/hgSession) -- [Public hubs](/cgi-bin/hgHubConnect#publicHubs) (to contribute your own, see - our [guidelines](/goldenPath/help/publicHubGuidelines.html)) -- [Contributed tracks](/docs/hubs/contributedTracks.html) for GenArk assemblies - -Relevant FAQs: - -- [Data File Formats](/FAQ/FAQformat.html) - see the formats supported by the Genome Browser - - -## Downloading data from the Genome Browser - -Beyond data visualization, the Genome Browser offers a wide variety of ways to access -and work with the underlying data: - -- The [download server](https://hgdownload.gi.ucsc.edu/downloads.html) provides - access to the data underlying the Genome Browser, - in addition to pairwise alignment and LiftOver chain files. -- Our [REST API](/goldenPath/help/api.html) can be used to retrieve data in JSON format. -- Our [public MySQL server](/goldenPath/help/mysql.html) allows command-line access to underlying data tables. -- We provide [command-line tools](https://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads) - for working with bigBed, bigWig, or other formats, - and command-line versions of our tools like `liftOver` or `blat`. - -We also provide scripts for creating your own -[mirror](/goldenPath/help/mirror.html) of the Genome Browser software and -databases, although it is often recommended to explore other methods of -visualizing your custom data as mirrors can require significant effort and -storage space to set up and maintain. - -Relevant FAQs: - -- [Data and Downloads](/FAQ/FAQdownloads.html) -- [Mirroring or Licensing the Genome Browser](/FAQ/FAQlicense.html) +The Genome Browser offers a web-based interface for visualizing genomic data on +a variety of genome assemblies. If you're new here, the tutorials below are +the fastest way to get started. + +## Tutorials + +| Tutorial | Description | +| - | - | +| [Genome Browser Basics](/docs/tutorials/gb101.html) | Learn the basics of the Genome Browser interface | +| [Gateway Page](/docs/tutorials/gatewayTutorial.html) | Find and switch between genome assemblies | +| [Table Browser](/docs/tutorials/tableBrowserTutorial.html) | Query and download Genome Browser data | +| [Custom Tracks](/docs/tutorials/customTrackTutorial.html) | Display your own annotations in the Genome Browser | + +Prefer video? Our [training page](/training/index.html) has short how-to +videos on common tasks like saving sessions, using BLAT and isPCR, and +finding SNPs in a gene. + +Looking up a term you don't recognize? Check our +[glossary](/docs/genomeBrowserGlossary.html). + +## Visualize your own data + +Display your own annotations alongside the data we host: + +- [Custom tracks](/cgi-bin/hgCustom) — the simpler option for displaying + your own annotations. See our + [documentation](/goldenPath/help/customTrack.html) to learn how to load + your own. +- [Track hubs](/cgi-bin/hgHubConnect#unlistedHubs) — more powerful and + configurable, ideal for many tracks or for sharing data publicly. Start + with our [Hub Basics](/docs/hubs/hubBasics.html) page, and validate your + hub with our [hub development tools](/cgi-bin/hgHubConnect#hubDeveloper). + +For both hubs and custom tracks, we provide storage through +[hub space](/cgi-bin/hgHubConnect#hubUpload). + +## Share your work + +Once you've configured a view, share it with collaborators or publish it +broadly: + +- [Links](/FAQ/FAQlink.html) — share a snapshot of your current view as a URL. +- [Sessions](/cgi-bin/hgSession) — save and share full Genome Browser + configurations. +- [Public hubs](/cgi-bin/hgHubConnect#publicHubs) — to contribute your own, + see our [guidelines](/goldenPath/help/publicHubGuidelines.html). +- [Contributed tracks](/docs/hubs/contributedTracks.html) — submit + annotations on [GenArk](https://hgdownload.gi.ucsc.edu/hubs/) assemblies. + +## Download data + +Access our underlying data outside the browser: + +- The [download server](https://hgdownload.gi.ucsc.edu/downloads.html) + provides the data underlying the Genome Browser, plus pairwise alignments + and LiftOver chain files. +- Our [REST API](/goldenPath/help/api.html) returns data in JSON format. +- [Command-line tools](https://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads) + for working with bigBed, bigWig, and other formats, plus standalone + versions of `liftOver`, `blat`, and others. + +## Get help + +- [Contact us](/contacts.html) — email, mailing lists, and other support + channels. +- [FAQ](/FAQ/) — common questions, including + [data file formats](/FAQ/FAQformat.html). +- Want a hands-on workshop at your institution? + [Get in touch](/contacts.html) about hosting one, in-person or virtual. +- Found a bug or have an idea? + [Submit a suggestion](/cgi-bin/hgUserSuggestion).