c5ff7a18c40453535ec9514b16da3d2f39a9a0cc jnavarr5 Fri Jan 30 16:18:23 2026 -0800 Moving the Hub Space announcement to the top for next week's release, refs #36290 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 84594473136..6c12ec3acba 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,81 @@ <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> <!-- ============= 2025 archived news ============= --> <a name="2026"></a> +<!-- +<a name="120525"></a> +<h2>Dec. 05, 2025 Hub Space: Host Your Track Hubs Directly on the Genome Browser</h2> +<p> +We are excited to introduce <a href="/cgi-bin/hgHubConnect#hubUpload">Hub Space</a>, a new +hosting service that allows users to upload and visualize track hub files directly on the UCSC +Genome Browser without relying on third-party hosting services such as Dropbox, Google Drive, or +AWS. +</p> + +<p> +<b>Hub Space Features:</b><br> +Each account is allocated 10 GB of storage space. While we strive to maintain uninterrupted +access, please maintain your own backups. Data persistence over the long term is not +guaranteed. To request additional storage space, please +<a href="/contacts.html">contact us</a>. +</p> + +<p> +<b>How to Use Hub Space:</b><br> +There are two primary ways to upload your files: +</p> + +<ol> + <li> + <b>Single file upload:</b> Upload individual binary-indexed files (bigBed, bigWig, BAM, VCF, + and other supported formats) for immediate visualization. + </li> + <li> + <b>Complete hub upload:</b> Upload an entire track hub along with all supporting files + (hub.txt, bigWig, bigBed, etc.) to visualize the hub. + </li> +</ol> + +<p> +If a hub.txt file is not provided when uploading data files, one is automatically generated. +The generated hub.txt file is configured with the +<a href="/goldenPath/help/trackDb/trackDbHub.html#useOneFile">useOneFile</a> trackDb setting, and +as a result, each hub is limited to a single genome assembly. Editing the generated hub.txt file is +not yet supported. To customize the hub configuration or data display, replace the generated hub.txt +file with your own version after uploading the data files. +</p> + +<p> +To get started with Hub Space, visit the +<a href="/cgi-bin/hgHubConnect#hubUpload">Track Data Hubs page</a> and +click on the "Hub Space" section. We would love to hear your feedback on this new feature. +Please <a href="/contacts.html">contact us</a> and let us know what you think! +</p> +--> + <a name="011526"></a> <h2>Jan. 15, 2026 New ENCODE cCREs track available for human (hg38)</h2> <p> We are proud to announce a new <a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=cCREs&position=default" target="_blank"> ENCODE Registry of cCREs (candidate Cis-Regulatory Elements)</a> container track for the hg38/GRCh38 genome as described in <a target="_blank" href="https://www.nature.com/articles/s41586-025-09909-9">Moore et al., <em>Nature</em> 2026</a>. This container contains candidate Cis-Regulatory Elements (cCREs) generated by the ENCODE Consortium during Phase 4 (ENCODE4) and Phase 3 (ENCODE3). The previous "ENCODE3 cCREs" track is retained for archival purposes. The tracks include both integrated (biosample-agnostic) and biosample-specific annotations derived from core epigenomic assays.</p> <div class="text-left"> <a href="https://genome.ucsc.edu/s/Lou/HBBexample" target=_blank> @@ -325,81 +376,30 @@ featuring data from Archaic Sequence Hub (ArcSeqHub). This track shows variants identified by ArcSeqHub's remapping of high-quality Altai Neanderthal and Denisovan genomes onto the hg38/GRCh38 genome. Variants are divided into two subtracks, one for Denisovian variants and another for Neanderthal variants. UCSC has removed those positions from the VCF without an alternate allele to show only variants that are present in the ancient genomes.</p> <div class="text-center"> <img src="/images/newsArchImages/ancientHominids.png" width='80%'></a> </div> <p> We would like to thank the <a href="http://www.arcseqhub.com/plot/-1/" target="_blank">ArcSeqHub</a> authors for making the data available. We would also like to thank Maximilian Haeussler and Matthew Speir for the creation and release of this track.</p> -<!-- -<a name="120525"></a> -<h2>Dec. 05, 2025 Hub Space: Host Your Track Hubs Directly on the Genome Browser</h2> -<p> -We are excited to introduce <a href="/cgi-bin/hgHubConnect#hubUpload">Hub Space</a>, a new -hosting service that allows users to upload and visualize track hub files directly on the UCSC -Genome Browser without relying on third-party hosting services such as Dropbox, Google Drive, or -AWS. -</p> - -<p> -<b>Hub Space Features:</b><br> -Each account is allocated 10 GB of storage space. While we strive to maintain uninterrupted -access, please maintain your own backups. Data persistence over the long term is not -guaranteed. To request additional storage space, please -<a href="/contacts.html">contact us</a>. -</p> - -<p> -<b>How to Use Hub Space:</b><br> -There are two primary ways to upload your files: -</p> - -<ol> - <li> - <b>Single file upload:</b> Upload individual binary-indexed files (bigBed, bigWig, BAM, VCF, - and other supported formats) for immediate visualization. - </li> - <li> - <b>Complete hub upload:</b> Upload an entire track hub along with all supporting files - (hub.txt, bigWig, bigBed, etc.) to visualize the hub. - </li> -</ol> - -<p> -If a hub.txt file is not provided when uploading data files, one is automatically generated. -The generated hub.txt file is configured with the -<a href="/goldenPath/help/trackDb/trackDbHub.html#useOneFile">useOneFile</a> trackDb setting, and -as a result, each hub is limited to a single genome assembly. Editing the generated hub.txt file is -not yet supported. To customize the hub configuration or data display, replace the generated hub.txt -file with your own version after uploading the data files. -</p> - -<p> -To get started with Hub Space, visit the -<a href="/cgi-bin/hgHubConnect#hubUpload">Track Data Hubs page</a> and -click on the "Hub Space" section. We would love to hear your feedback on this new feature. -Please <a href="/contacts.html">contact us</a> and let us know what you think! -</p> ---> - <a name="120325"></a> <h2>Dec. 03, 2025 New gnomAD Missense Deleteriousness Prediction by Constraint (MPC) track for hg19</h2> <p> We are happy to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=gnomadMpc" target="_blank">gnomAD Missense Deleteriousness Prediction by Constraint (MPC) track</a> for hg19, now available in the <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=gnomadSuper" target="_blank">gnomAD superTrack</a>. This track shows a score that tries to identify missense-depleted regions using the patterns of rare missense variation in 125,748 gnomAD v2.1.1 exomes, compared to a null mutational model. Missense-depleted regions are enriched for ClinVar pathogenic variants, de novo missense variants in individuals with neurodevelopmental disorders (NDDs), and complex trait heritability. This track can be used to aid in interpreting missense variants.</p> <p> Transcript regions with constraint predictions are colored using the viridis palette, where yellow