0e28eac3fe0eaa0cdd5afec9c683e883e8836f95 jnavarr5 Tue Sep 1 13:53:03 2026 -0700 Add Sep. 1 2026 news announcement for the new faceted composite interface, with screenshot and indexNews entry, refs #36320 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 0752b27ad9d..17b6564a17b 100644 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,114 @@ <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2026 archived news ============= --> <a name="2026"></a> +<a name="090126"></a> +<h2>Sep. 1, 2026 New faceted interface for large composite tracks</h2> +<p> +We are pleased to announce +<a href="/docs/hubs/facetedComposite.html" target="_blank">faceted composites</a>, a new +interface for composite tracks that hold very large numbers of subtracks. The standard +composite works well for somewhere between 20 and 50 subtracks, but it becomes unwieldy +once the count runs into the hundreds to thousands. A faceted composite is an alternative +display for those cases: facets along the left side filter the collection while a +paginated table on the right lists the subtracks that match, letting users narrow +thousands of entries down to the handful relevant to their work. The individual-experiment +tracks in the ENCODE4 Regulation collection, <a href="#072226">announced in July 2026</a>, +already use this interface. Faceted composites are configured entirely through trackDb +settings, so any hub developer can build one. +</p> + +<div class="text-center" style="margin-top: 1.5em;"> +<a href="/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeReg4Epigenetics" target="_blank"> +<img alt="Faceted composite interface showing facets, search boxes, and a paginated subtrack table" +src="/images/newsArchImages/facetedComposite.png" width='75%'></a> +<p class="gbsCaption"><em>The faceted composite interface on the ENCODE4 +DNase/ATAC/Histone/CTCF (Indiv.) track. Facets on the left filter the 6,353 subtracks, +and the table lists those that match.</em></p> +</div> + +<p> +A faceted composite otherwise behaves like an ordinary composite, with two differences: +</p> +<ul> + <li>it does not use views or subgroups</li> + <li>it draws its facets from a web-accessible tab-separated metadata file named in the + <code>metaDataUrl</code> setting</li> +</ul> + +<p> +Adding <code>compositeTrack faceted</code> to a composite stanza turns on the interface. A +<code>primaryKey</code> setting names the column of that file which identifies each +subtrack, and subtracks are named <code><parent>_<primaryKey value></code> to +tie each one to its metadata row. Because there are no views, the subtracks of a single +faceted composite can mix data types, such as signal and peak files, in one container. +</p> + +<p> +Underscore prefixes on the field names in the metadata file control where each field +shows up: +</p> + +<table class="stdTbl"> + <tr><th>Field name in the metadata file</th><th>Facet on the page</th> + <th>Search box in the table</th></tr> + <tr><td><code>tissue</code></td><td>yes</td><td>yes</td></tr> + <tr><td><code>_date</code></td><td>no</td><td>yes</td></tr> + <tr><td><code>__count</code></td><td>no</td><td>no</td></tr> +</table> + +<p> +Two optional settings extend the interface: +</p> +<ul> + <li><code>dataTypes</code> – groups several files per sample, so a single row of + the subtrack table can turn on a signal track and a peak track together</li> + <li><code>subtrackUrls</code> – turns metadata values into links, which is useful + for accession numbers or protocol identifiers</li> +</ul> + +<p> +Our new <a href="/docs/hubs/facetedComposite.html" target="_blank">Faceted Composite +Tracks</a> documentation page walks through building one, with an +<a href="/cgi-bin/hgTracks?db=hg38&position=chr7:155799529-155812871&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubFacetedComposite/hub.txt" +target="_blank">example hub</a> that can be loaded directly into the browser. The complete +reference for each setting lives in our +<a href="/goldenPath/help/trackDb/trackDbHub.html#faceted_composite" target="_blank">trackDb +documentation</a>, and our <a href="/docs/hubs/hubBasics.html" target="_blank">Hub +Basics</a> page is a good starting point if you are new to building hubs. +</p> + +<p> +We would like to thank Andrew Smith at the University of Southern California, who +contributed the original implementation of this interface, and Jonathan Casper, who +developed it into the version released at the UCSC Genome Browser. We also thank +Lou Nassar, Gerardo Perez, Clay Fischer, Brian Raney, Max Haeussler, and Jairo +Navarro for testing, feedback, and documentation. +</p> + <a name="082826"></a> <h2>Aug. 28, 2026 Deleteriousness Predictions: popEVE and EVE for hg38</h2> <p> We are pleased to announce the release of two new proteome-wide missense variant effect prediction tracks for hg38: <a href="/cgi-bin/hgTrackUi?db=hg38&g=popEve&position=default" target="_blank">popEVE</a> and <a href="/cgi-bin/hgTrackUi?db=hg38&g=eve&position=default" target="_blank">EVE</a>. Both are deep generative models that predict variant pathogenicity by learning patterns of natural sequence variation across species, without relying on clinical labels. </p> <h3>EVE</h3> <p> <a href="https://evemodel.org" target="_blank">EVE</a> (Evolutionary model of Variant Effect) is a deep generative model that predicts the pathogenicity of missense variants by learning patterns of