979f7584699eedd743c90a7cf59d9fac44de845d dschmelt Thu Feb 24 23:11:26 2022 -0800 Adding info and announcement for drug resistance track refs #28889 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 2dc11e1..a218509 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,44 @@ <div class="col-sm-3"> <ul> <li><a href="#2006">2006 News</a></li> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2001">2001</a>-<a href="#2002">2002 News</a></li> </ul> </div> </div> </div> <!-- ============= 2022 archived news ============= --> <a name="2022"></a> +<a name="02252022"></a> +<h2>Feb, 25, 2022 &nbps; New COVID track on Drug Resistance Mutations</h2> +<p> +We have just added the <a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=resist">Drug Resistance</a> +track to the SARS-CoV-2 (COVID-19) genome. This track shows 5 amino acid variants +documented to confer drug treatment resistance to Remdesivir. Try it yourself:</p> +<p> +<a href=" https://genome.ucsc.edu/s/view/DrugResistance">https://genome.ucsc.edu/s/view/DrugResistance</a> +</p> +<p>We would like to thank data contributor Paul Gordon, for making the data +accessible on his <a href="https://people.ucalgary.ca/~gordonp/remdesivir_failure-RdRp.html"> +University of Calgary website</a>.</p> + + <a name="022222"></a> <h2>Feb. 22, 2022 Recommended Track Sets paper</h2> <p> We are pleased to announce a new paper about our Recommended Tracks Set feature, available on GRCh37/hg19, which collects related clinical tracks to help investigate variants. The paper, <a href="https://doi.org/10.1002/humu.24335" target="_blank">Variant interpretation: UCSC Genome Browser Recommended Track Sets</a>, covers how this new feature can facilitate the interpretation of variants for clinicians.</p> <p> Track Sets allow a user to quickly swap out the on-screen annotations they may be looking at for a different set of tracks relevant to specific medical scenarios: investigating single nucleotide variants in coding regions (Clinical SNVs), structural copy number variants (Clinical CNVs), and functional aspects of non-coding variants (Non-coding SNVs).</p> <p class ="text-center"> <a href="https://doi.org/10.1002/humu.24335"> @@ -204,44 +218,44 @@ </p> <p> These tracks represent genome-wide predicted binding sites for transcription factor binding profiles in the <a href="https://jaspar.genereg.net/about/" target="_blank">JASPAR CORE collection</a>. JASPAR CORE is an open-source database containing a curated, non-redundant set of binding profiles derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. </p> <p> The JASPAR database is a joint effort between several labs (please see the latest <a href="https://www.ncbi.nlm.nih.gov/pubmed/34850907" target="_blank">JASPAR paper</a>). Binding site predictions and UCSC tracks were computed by the <a href="http://cisreg.ca/" target="_blank">Wasserman Lab</a>. We would like to thank Daniel Schmelter and Jairo Navarro at UCSC for building and testing these tracks.</p> +<!-- ============= 2021 archived news ============= --> +<a name="2021"></a> + <a name="122021"></a> <h2>Dec. 20, 2021 Last of three blog posts about new GenArk hubs</h2> <p> We are pleased to announce the third blog post in a three-part series about our new GenArk Assembly Hubs. This <a href="https://genome-blog.soe.ucsc.edu/blog/2021/12/20/genark-hubs-part-3/" target="_blank">final installment</a> provides some explanation of the technical details behind the process. The <a href="https://bit.ly/UCSC_blog_GenArk1">first post</a> was about accessing the data, and the <a href="https://bit.ly/UCSC_blog_GenArk2">second post</a> shared examples of using the hub's data with BLAT, PCR, and External Tools.</p> -<!-- ============= 2021 archived news ============= --> -<a name="2021"></a> - <a name="121621"></a> <h2>Dec. 16, 2021 Track Hub Filters Quick Start Guide</h2> <p> We are pleased to announce a help page specific to building filters on Track Hubs. <a href="help/hgTrackHubHelp.html#Intro">Track Hubs</a> are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser. Track Hubs allow a lab to share and host all their genomic data (<a href="help/bam.html">BAMs</a>, <a href="help/vcf.html">VCFs</a>, ect.) via a single Genome Browser link. Such links can load multiple hubs and even be combined with a position parameter to easily reference laboratory data around a gene of interest, see examples in a recent <a href="https://bit.ly/UCSC_blog_sharing">blog bost</a> about sharing data with URLs.</p> <p> The <a href="help/hubQuickStartFilter.html">Track Hub Filters Quick Start Guide</a> provides example hubs employing new extensive <a href="help/trackDb/trackDbHub.html#filter">filter</a> settings available for Track Hubs.</p> <p>