e5759993329b6e609e9ab825991a90283e714088 mspeir Wed Sep 9 11:17:57 2026 -0700 Help pages: fix broken internal links and restore anchors people still cite, refs #38062 Three groups of anchor problems on the help and FAQ pages. Broken internal links, five pages: posters.html listed a 2022 section that does not exist (no 2022 posters), api.html listed REST and JSON separately after the two sections were merged, docker.html pointed at a #UsrAcct section that is not on that page, FAQgenes.html had a capitalized #ncbiRefSeq where the anchor is #ncbiRefseq, and the genomes.txt settings rows in trackDbHub.v3.html carried no anchors so its own "genome" link missed. Retired anchors that are still cited in twenty years of answers on the genome list. Content moved to its own page and the old anchor was deleted rather than left behind, so the citations land at the top of the page. Reattached seven numeric FAQformat anchors to the Topics entry linking to each format's page. BED, PSL, GFF and GTF were removed from the custom track page in 2012 and never added back to its list of supported formats; added them with the old anchors, which fixes customTrack.html and hgTracksHelp.html together since both include customTrackText.html. Also restored #lines there, and #Session on hgTrackHubHelp.html and #link4 on FAQlink.html. Section anchors on six pages that had none, so a support answer can link to one part of them: bam.html, hic.html, bedgraph.html, ftp.html, net.html and trackDbIndexBb.html. Skipped quickLiftChain.html, oligoMatch.html and cutters.html, which are track description fragments included into the details page rather than standalone pages. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/goldenPath/help/posters.html src/hg/htdocs/goldenPath/help/posters.html index 44a596e5c3f..896ccd7288b 100755 --- src/hg/htdocs/goldenPath/help/posters.html +++ src/hg/htdocs/goldenPath/help/posters.html @@ -1,563 +1,562 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser Poster Gallery" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <style> /* === Poster box styling === */ .poster-box { text-align: center; /* center text and image inside poster cell */ padding-bottom: 15px; /* add some space under each poster */ } /* clickable image itself should only be the visible PNG */ .poster-box a img { display: inline-block; /* ensures the clickable area = only the image */ } /* wrapper link around poster content */ .poster-link { text-decoration: none; display: inline-block; /* shrink to contents */ text-align: center; color: inherit; /* inherit surrounding text color */ } /* conference label */ .poster-conf { display: block; font-size: 18px; font-weight: bold; } /* poster title under conference name */ .poster-title { display: block; font-size: 14px; color: #333; } /* poster preview image (thumbnail) */ .poster-img { display: block; margin: 0 auto; max-width: 400px; height: auto; } /* larger preview version for certain posters */ .poster-img.large { max-width: 600px; /* new larger preview width */ width: 100%; height: auto; } /* === Collapsible year button styling === */ .collapsible { background-color: #4C759C; color: white; cursor: pointer; padding: 8px 20px; width: 100%; text-align: left; font-size: 20px; font-weight: bold; border: none; } .collapsible:hover { background-color: #327DE4; } .collapsible:after { content: '\002B'; float: right; margin-left: 5px; } .collapsible.active:after { content: '\2212'; } .collapseMe { padding: 0 18px; max-height: 0; overflow: hidden; transition: max-height 0.3s ease, padding 0.3s ease; } .collapseMe.open { padding: 12px 18px 24px; } /* Center year navigation */ .year-nav { display: flex; justify-content: center; gap: 40px; margin-bottom: 20px; } .year-nav ul { list-style: none; /* remove bullets */ padding: 0; margin: 0; } .year-nav a { text-decoration: none; font-weight: bold; font-size: 20px; color: #004080; /* UCSC dark blue */ transition: color 0.2s ease; } .year-nav a:hover { color: #327DE4; /* lighter blue on hover */ text-decoration: underline; } .year-nav li { margin: 6px 0; } .year-nav .col-sm-3 { padding-left: 120px; padding-right: 120px; } /* small responsive */ @media (max-width: 768px) { .col-md-6, .col-md-4, .col-md-12 { width: 100%; display: block; } .poster-img { width: 320px; } } /* Reserved for additional genome-specific styles */ .otherGenomes { </style> <h1>UCSC Genome Browser Poster Gallery</h1> <!-- ===== Year Navigation Menu (4 columns, 2025-2015) ===== --> <div class="container year-nav"> <div class="row"> <div class="col-sm-3"> <ul> <li><a href="#2026">2026</a></li> <li><a href="#2025">2025</a></li> <li><a href="#2024">2024</a></li> </ul> </div> <div class="col-sm-3"> <ul> <li><a href="#2023">2023</a></li> - <li><a href="#2022">2022</a></li> <li><a href="#2021">2021</a></li> </ul> </div> <div class="col-sm-3"> <ul> <li><a href="#2020">2020</a></li> <li><a href="#2019">2019</a></li> <li><a href="#2018">2018</a></li> </ul> </div> <div class="col-sm-3"> <ul> <li><a href="#2017">2017</a></li> <li><a href="#2016">2016</a></li> <li><a href="#2015">2015</a></li> </ul> </div> </div> </div> <!-- ===== Poster Sections ===== --> <!-- ======= YEAR 2026 ======= --> <button id="2026" class="collapsible active">2026</button> <div class="collapseMe" > <div class="row"> <div class="col-md-6"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/BiologyofGenomes2026.pdf" target="_blank" rel="noopener"> <span class="poster-conf">Biology of Genomes 2026</span> <span class="poster-title">UCSC Genome Browser 2026: Storage for your track hubs, lift any tracks, edit annotations & new tracks: long-read SVs, short-read SNVs, tandem repeats and NMD escape</span> <img class="poster-img" src="/goldenPath/posters/BiologyofGenomes2026_thumb.png" alt="Biology of Genomes 2026 preview"> </a> </div> </div> <div class="col-md-6"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/ISV2026.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ISV 2026</span> <span class="poster-title">UCSC Genome Browser 2026: Latest resources for variant analysis</span> <img class="poster-img" src="/goldenPath/posters/ISV2026_thumb.png" alt="ISV 2026 preview"> </a> </div> </div> </div> </div> <!-- ======= YEAR 2025 ======= --> <button id="2025" class="collapsible active">2025</button> <div class="collapseMe" > <div class="row"> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/ASHG2025.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ASHG 2025</span> <span class="poster-title">UCSC Genome Browser: Latest resources for variant interpretation</span> <img class="poster-img" src="/goldenPath/posters/ASHG2025_thumb.png" alt="ASHG 2025 preview"> </a> </div> </div> <div class="col-md-4"> <div class="poster-box"> <!-- Poster link (PDF) + preview (PNG) --> <a class="poster-link" href="/goldenPath/posters/trackDecorators_ESHG2025.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ESHG 2025</span> <span class="poster-title">UCSC Genome Browser Track Decorators</span> <img class="poster-img" src="/goldenPath/posters/trackDecorators_ESHG2025_thumb.png" alt="ESHG 2025 poster preview"> </a> </div> </div> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/BiologyofGenomes2025.pdf" target="_blank" rel="noopener"> <span class="poster-conf">Biology of Genomes 2025</span> <span class="poster-title">UCSC Genome Browser: HubSpace Track Storage</span> <img class="poster-img" src="/goldenPath/posters/BiologyofGenomes2025_thumb.png" alt="Biology of Genomes 2025 preview"> </a> </div> </div> </div> </div> <!-- ======= YEAR 2024 ======= --> <button id="2024" class="collapsible active">2024</button> <div class="collapseMe" > <div class="row"> <div class="col-md-4"> <div class="poster-box"> <!-- Poster link (PDF) + preview (PNG) --> <a class="poster-link" href="/goldenPath/posters/BiologyofGenomes2024.pdf" target="_blank" rel="noopener"> <span class="poster-conf">Biology of Genomes 2024</span> <span class="poster-title">Viewing Human Pangenome Research Consortium (HPRC) data on the UCSC Genome Browser</span> <img class="poster-img" src="/goldenPath/posters/BiologyofGenomes2024_thumb.png" alt="Biology of Genomes 2024 preview"> </a> </div> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/veptc2024.pdf" target="_blank" rel="noopener"> <span class="poster-conf">VEPTC 2024</span> <span class="poster-title">UCSC Genome Browser: Latest developments for variant interpretation</span> <img class="poster-img" src="/goldenPath/posters/veptc2024_thumb.png" alt="VEPTC 2024 preview"> </a> </div> </div> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/ICTE2024.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ICTE 2024</span> <span class="poster-title">Visualizing transposable elements with the UCSC Genome Browser</span> <img class="poster-img" src="/goldenPath/posters/ICTE2024_thumb.png" alt="ICTE 2024 preview"> </a> </div> </div> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/ISV2024.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ISV 2024</span> <span class="poster-title">UCSC Genome Browser: Latest resources for variant interpretation</span> <img class="poster-img" src="/goldenPath/posters/ISV2024_thumb.png" alt="ISV 2024 preview"> </a> </div> </div> </div> </div> <!-- ======= YEAR 2023 ======= --> <button id="2023" class="collapsible active">2023</button> <div class="collapseMe" > <div class="row"> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/genomeBrowserBoG2023.pdf" target="_blank" rel="noopener"> <span class="poster-conf">Biology of Genomes 2023</span> <span class="poster-title">Visualizing genomic rearrangements with the UCSC Genome Browser snakes display</span> <img class="poster-img" src="/goldenPath/posters/genomeBrowserBoG2023_thumb.png" alt="BoG 2023 preview"> </a> </div> </div> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/genomeBrowserASHG2023.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ASHG 2023</span> <span class="poster-title">quickLift: Lifting UCSC Genome Browser annotations on demand</span> <img class="poster-img" src="/goldenPath/posters/genomeBrowserASHG2023_thumb.png" alt="ASHG 2023 preview"> </a> </div> </div> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/CSHL_GenomeInformatics_2023.pdf" target="_blank" rel="noopener"> <span class="poster-conf">CSHL 2023</span> <span class="poster-title">GenArk: Towards A Million Genome Browsers</span> <img class="poster-img" src="/goldenPath/posters/CSHL_GenomeInformatics_2023_thumb.png" alt="CSHL 2023 preview"> </a> </div> </div> </div> </div> <!-- ======= YEAR 2021 ======= --> <button id="2021" class="collapsible active">2021</button> <div class="collapseMe" > <div class="row"> <div class="col-md-12"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/CSHL_2021.pdf" target="_blank" rel="noopener"> <span class="poster-conf">CSHL 2021</span> <span class="poster-title">UCSC Genome Browser in the Cloud (GBiC)</span> <img class="poster-img" src="/goldenPath/posters/CSHL_2021_thumb.png" alt="CSHL 2021 preview"> </a> </div> </div> </div> </div> <!-- ======= YEAR 2020 ======= --> <button id="2020" class="collapsible active">2020</button> <div class="collapseMe" > <div class="row"> <div class="col-md-6"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/PAG_Poster_API_2020.pdf" target="_blank" rel="noopener"> <span class="poster-conf">PAG 2020</span> <span class="poster-title">UCSC Genome Browser REST API Returning Assembly Hub JSON Data</span> <img class="poster-img" src="/goldenPath/posters/PAG_Poster_API_2020_thumb.png" alt="PAG 2020 preview"> </a> </div> </div> <div class="col-md-6"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/ASHG2020.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ASHG 2020</span> <span class="poster-title">Visualizing Hi-C chromatin interactions in the UCSC Genome Browser</span> <img class="poster-img" src="/goldenPath/posters/ASHG2020_thumb.png" alt="ASHG 2020 preview"> </a> </div> </div> </div> </div> <!-- ======= YEAR 2019 ======= --> <button id="2019" class="collapsible active">2019</button> <div class="collapseMe" > <div class="row"> <div class="col-md-6"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/UCSC_PAG_2019_AssemblyHub.pdf" target="_blank" rel="noopener"> <span class="poster-conf">PAG 2019</span> <span class="poster-title">Annotating Variants and Displaying Multiple Alignments on Your Assemblies Using the UCSC Genome Browser</span> <img class="poster-img" src="/goldenPath/posters/UCSC_PAG_2019_AssemblyHub_thumb.png" alt="PAG 2019 preview"> </a> </div> </div> <div class="col-md-6"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/ASHG_2019_Interact.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ASHG 2019</span> <span class="poster-title">UCSC Genome Browser: New Interact Format and GeneHancer Data</span> <img class="poster-img" src="/goldenPath/posters/ASHG_2019_Interact_thumb.png" alt="ASHG 2019 preview"> </a> </div> </div> </div> </div> <!-- ======= YEAR 2018 ======= --> <button id="2018" class="collapsible active">2018</button> <div class="collapseMe" > <div class="row"> <div class="col-md-6"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/UCSC_BoG_2018_GtexPoster.pdf" target="_blank" rel="noopener"> <span class="poster-conf">Biology of Genomes 2018</span> <span class="poster-title">GTEx resources and new 'barChart' and 'interacton' track displays inspired by GTEx</span> <img class="poster-img" src="/goldenPath/posters/UCSC_BoG_2018_GtexPoster_thumb.png" alt="BoG 2018 preview"> </a> </div> </div> <div class="col-md-6"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/UcscPostDoc_2018.pdf" target="_blank" rel="noopener"> <span class="poster-conf">UCSC PostDoc 2018</span> <span class="poster-title">Visualizing RNA-seq data in the UCSC Genome Browser</span> <img class="poster-img" src="/goldenPath/posters/UcscPostDoc_2018_thumb.png" alt="PostDoc 2018 preview"> </a> </div> </div> </div> </div> <!-- ======= YEAR 2017 ======= --> <button id="2017" class="collapsible active">2017</button> <div class="collapseMe" > <div class="row"> <div class="col-md-12"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/GenomeInformatics2017.pdf" target="_blank" rel="noopener"> <span class="poster-conf">Genome Informatics 2017</span> <span class="poster-title">HGVS variant nomenclature in the UCSC Genome Browser</span> <img class="poster-img" src="/goldenPath/posters/GenomeInformatics2017_thumb.png" alt="Genome Informatics 2017 preview"> </a> </div> </div> </div> </div> <!-- ======= YEAR 2016 ======= --> <button id="2016" class="collapsible active">2016</button> <div class="collapseMe" > <div class="row"> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/ACMGposter2016.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ACMG 2016</span> <span class="poster-title">Visualize and Analyze Your Genomic Data on the UCSC Genome Browser</span> <img class="poster-img" src="/goldenPath/posters/ACMGposter2016_thumb.png" alt="ACMG 2016 preview"> </a> </div> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/GTEX_2016_Poster.pdf" target="_blank" rel="noopener"> <span class="poster-conf">GTEx 2016</span> <span class="poster-title">GTEx Data in the UCSC Genome Browser 2016 Update</span> <img class="poster-img" src="/goldenPath/posters/GTEX_2016_Poster_thumb.png" alt="GTEx 2016 preview"> </a> </div> </div> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/PosterIchg2016.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ICHG 2016</span> <span class="poster-title">Visualize and Analyze Your Genomic Data on the UCSC Genome Browser</span> <img class="poster-img" src="/goldenPath/posters/PosterIchg2016_thumb.png" alt="ICHG 2016 preview"> </a> </div> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/CrisporCshl2016.pdf" target="_blank" rel="noopener"> <span class="poster-conf">CSHL 2016</span> <span class="poster-title">Evaluation of off-target and on-target scoring algorithms: Integration into crispor.org and the UCSC Genome Browser</span> <img class="poster-img" src="/goldenPath/posters/CrisporCshl2016_thumb.png" alt="CSHL 2016 preview"> </a> </div> </div> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/Multi-region-BoG2016.pdf" target="_blank" rel="noopener"> <span class="poster-conf">Biology of Genomes 2016</span> <span class="poster-title">New UCSC Genome Browser Views: Exon-Only, Gene-Only, Alternate Haplotypes, and Custom Regions</span> <img class="poster-img" src="/goldenPath/posters/Multi-region-BoG2016_thumb.png" alt="BoG 2016 preview"> </a> </div> </div> </div> </div> <!-- ======= YEAR 2015 ======= --> <button id="2015" class="collapsible active">2015</button> <div class="collapseMe" > <div class="row"> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/Acmg2015poster.pdf" target="_blank" rel="noopener"> <span class="poster-conf">ACMG 2015</span> <span class="poster-title">UCSC Genome Browser and Variant Annotation Integrator</span> <img class="poster-img" src="/goldenPath/posters/Acmg2015poster_thumb.png" alt="ACMG 2015 preview"> </a> </div> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/BioengSymp2015Poster.pdf" target="_blank" rel="noopener"> <span class="poster-conf">UC-wide Bioeng 2015</span> <span class="poster-title">Use The UCSC Genome Browser To Visualize And Analyze Your Genomic Data</span> <img class="poster-img" src="/goldenPath/posters/BioengSymp2015Poster_thumb.png" alt="Bioeng 2015 preview"> </a> </div> </div> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/G10K2015.pdf" target="_blank" rel="noopener"> <span class="poster-conf">Genome 10K 2015</span> <span class="poster-title">Assembly Hubs and Genome Browser in a Box Makes Viewing Private Annotations and Custom Sequences Easy</span> <img class="poster-img" src="/goldenPath/posters/G10K2015_thumb.png" alt="G10K 2015 preview"> </a> </div> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/GTEX2015Poster.pdf" target="_blank" rel="noopener"> <span class="poster-conf">GTEx 2015</span> <span class="poster-title">GTEx Data in the UCSC Genome Browser</span> <img class="poster-img" src="/goldenPath/posters/GTEX2015Poster_thumb.png" alt="GTEx 2015 preview"> </a> </div> </div> <div class="col-md-4"> <div class="poster-box"> <a class="poster-link" href="/goldenPath/posters/BoG2015DataIntegrator.pdf" target="_blank" rel="noopener"> <span class="poster-conf">BoG 2015</span> <span 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