67255df25296381bdd716c760d255eb45c984bab brianlee Wed Nov 4 10:25:43 2020 -0800 Adding links to news on covid19 and changing some links based on htmlCheck checkLink diff --git src/hg/htdocs/covid19.html src/hg/htdocs/covid19.html index 56df441..aff5194 100755 --- src/hg/htdocs/covid19.html +++ src/hg/htdocs/covid19.html @@ -20,139 +20,147 @@ on March 11, 2020. </p> <p> Genome sequencing of thousands of viral samples has helped researchers study mechanisms of infection, transmission and response of the human immune system. Since the beginning of SARS-CoV-2 circulation in humans, the viral genome has been accummulating mutations. Compared to other RNA viruses its mutation rate is low, but enough variants are known to determine how samples cluster into groups and how they are related (see COVID-19 transmission map). </p> <p> We at the <a target="_blank" href="https://ucscgenomics.soe.ucsc.edu/">UC Santa Cruz Genomics Institute</a> are responding to the urgency of supporting biomedical research aimed at developing treatments and a vaccine for this devastating illness by fast-tracking visualization of genome sequences and analyses in the -<a target="_blank" href="../cgi-bin/hgGateway?db=wuhCor1">UCSC Genome Browser for SARS-Cov-2</a>. +<a target="_blank" href="/cgi-bin/hgGateway?db=wuhCor1">UCSC Genome Browser for SARS-Cov-2</a>. Moreover, we are incorporating relevant biomedical datasets such as single-cell lung gene expression into the -<a target="_blank" href="../singlecell.html">UCSC Cell Browser</a>, and are creating data tracks +<a target="_blank" href="/singlecell.html">UCSC Cell Browser</a>, and are creating data tracks of <a target="_blank" href="#covidHgiGwas">COVID-19 annotations in our Human Genome Browsers</a> as datasets become publicly available. These annotations can further understanding of the human genetic determinants of infection susceptibility, disease severity, and outcomes. </p> <p> A manuscript describing <a href="https://www.nature.com/articles/s41588-020-0700-8" target="_blank"> The UCSC SARS-CoV-2 Genome Browser</a>, was published in the September 9 issue of <em>Nature Genetics</em>. </p> </div> <div class="col-md-6"> <img class="text-center" alt="COVID-19 transmission as of May 30, 2020, from Nextstrain" - src="../images/covid19/covid19-transmission.may30_2020.nextstrain.png" + src="/images/covid19/covid19-transmission.may30_2020.nextstrain.png" style="margin-bottom: 5px !important"> <div style="text-align: right; line-height: 1"> <font SIZE=-1><em>COVID-19 transmission as of May 30, 2020</em><BR> </font> <font SIZE=-2> <A HREF="https://nextstrain.org" TARGET=_blank>Latest situation report from Nextstrain.org</a> </font> </div> </div> </div> <style> img { width: 100%; margin: 15px 0 !important; } </style> <div class="row"> <!-- Genome browser --> <div class="col-md-6"> <h2>UCSC Genome Browser view of SARS-CoV-2 genomic datasets</h2> - <a href="../cgi-bin/hgTracks?db=wuhCor1" target="_blank"> - <img src="../images/sarsCov2SpikeProteinsSession.png"></a> + <a href="/cgi-bin/hgTracks?db=wuhCor1" target="_blank"> + <img src="/images/sarsCov2SpikeProteinsSession.png"></a> <br> Video tutorial: Using the <a href = http://bit.ly/ucscVid20 target = _blank>coronavirus browser</a>. </div> <!-- Cell browser --> <div class="col-md-6"> <h2>COVID-19 and Lung gene expression data in the UCSC Cell Browser:</h2> <p>COVID-19 Datasets: <ul> <li><a href="https://covid19-balf.cells.ucsc.edu" target="_blank">Bronchoalveolar Immune Cells in COVID-19</a> <li><a href="https://covid-airways.cells.ucsc.edu" target="_blank">COVID-19 Airways</a> <li><a href="https://covid19-influenza-response.cells.ucsc.edu" target="_blank">COVID-19 and Influenza Immunophenotyping</a> <li><a href="https://covid19atlas.cells.ucsc.edu" target="_blank">COVID-19 Cell Atlas</a> <li><a href="https://scarface.cells.ucsc.edu" target="_blank">COVID-19 SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs)</a> <li><a href="https://hca-lungmap-integrated.cells.ucsc.edu" target="_blank">HCA-LungMAP COVID-19 Integrated Analysis</a> </ul> <p><a href="https://cells.ucsc.edu/?bp=lung" target="blank">Other Lung datasets in the Cell Browser</a> </div> </div> <h2 id="news">News</h2> <ul> +<li> +<b>October 21, 2020</b>: +<a target="_blank" href="goldenPath/newsarch.html#102120"> +New gene models, immunology, pathogenicity, and conservation annotation tracks</a> +have been released. Click the above link to directly access track description pages +for specific track titles such as PhyloCSF Genes, Weizman ORFs, icSHAPE RNA Structure, +Validated epitopes from IEDB, and various Phylogenetic Tree tracks. +</li> <li id="covidHgiGwas"> <b>September 22, 2020</b>: First COVID-19-related annotation track on UCSC human genome browser: -<a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=covidHgiGwas" target="_blank"> +<a href="/cgi-bin/hgTrackUi?db=hg38&g=covidHgiGwas" target="_blank"> COVID-19 GWAS</a>: GWAS meta-analyses of studies contributed by multiple partners world-wide (18 in this release), as part of the <a target="_blank" href="https://www.covid19hg.org">COVID-19 Host Genetics Initiative</a>, a collaborative effort to facilitate the generation, analysis and sharing of COVID-19 host genetics research. </li> <li> <b>September 9, 2020</b>: The manuscript describing the <a href="https://www.nature.com/articles/s41588-020-0700-8" target="_blank"> The UCSC SARS-CoV-2 Genome Browser</a>, is now published in <em>Nature Genetics</em>. </li> <li> <b>August 7, 2020</b>: -<a target="_blank" href="https://genome.ucsc.edu/goldenPath/newsarch.html#080720"> +<a target="_blank" href="/goldenPath/newsarch.html#080720"> Eight new annotation tracks</a>, presenting information about duplication regions, sequencing, gene identities, plasmid constructs, protein contact sites, and variant distribution.</li> <li> <b>July 7, 2020</b>: Annotation tracks released: <a target="_blank" -href="https://genome.ucsc.edu/goldenPath/newsarch.html#070720"> +href="/goldenPath/newsarch.html#070720"> PhyloCSF (Codon Substitution Frequency), Microdeletions, and Human CoV</a> (multiple alignment of SARS-CoV-2, SARS-CoV-1, MERS, and three other human-infecting coronaviruses) </li> <li><b>May 29, 2020</b>: Public track hub <a target="_blank" href="http://ftp.ebi.ac.uk/pub/databases/gencode/covid19_trackhub/COVID19_Hub.html"> GENCODE annotation of COVID-19 associated genes</a> released. View in <a target="_blank" -href="../cgi-bin/hgTracks?hubUrl=http://ftp.ebi.ac.uk/pub/databases/gencode/covid19_trackhub/hub.txt&genome=hg38&position=lastDbPos" > +href="/cgi-bin/hgTracks?hubUrl=http://ftp.ebi.ac.uk/pub/databases/gencode/covid19_trackhub/hub.txt&genome=hg38&position=lastDbPos" > browser</a>. </li> <li><a target="_blank" href="goldenPath/newsarch.html#051220">Video: Coronavirus Browser SARS CoV-2</a></li> <li><a target="_blank" href="goldenPath/newsarch.html#050420">May data release for SARS-CoV-2 genome browser</a></li> <li><a target="_blank" href="goldenPath/newsarch.html#040320">April data release for SARS-CoV-2 genome browser</a></li> </ul> <h2 id="related">Related publications and data resources</h2> <ul> <li> Preprints of research manuscripts: @@ -219,31 +227,31 @@ <a target="_blank" href="https://www.nature.com/articles/d41586-020-01221-y"> The Race for Coronavirus Vaccines</a> </li> <li> <a target="_blank" href="https://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html"> Inside the Coronavirus Genome</a>, and <a target="_blank" href="https://www.nytimes.com/interactive/2020/04/30/science/coronavirus-mutations.html"> How Coronavirus Mutates and Spreads</a>, The New York Times </li> </ul> <h2 id="funding">Funding</h2> <p> -The <a target="_blank" href="https://genome.ucsc.edu"> +The <a target="_blank" href=".."> UCSC Genome Browser</a> is a publicly available web resource serving the research community since July 2000. Both the Genome Browser and UCSC Cell Browser are funded by the <a target="_blank" href="https://www.genome.gov/">NIH National Human Genome Research Institute</a>. In addition to this funding, the COVID-19 projects here are funded by generous supporters including: several anonymous donors; Pat and Roland Rebele; Eric and Wendy Schmidt by recommendation of the <a target="_blank" href="https://schmidtfutures.com/">Schmidt Futures</a> program; the Center for Information Technology Research in the Interest of Society (<a target="_blank" href="https://citris-uc.org/">CITRIS</a>); and the University of California Office of the President (<a target="_blank" href="https://www.universityofcalifornia.edu/uc-system/office-of-the-president">UCOP</a>). To contribute, click <a target="_blank" href="https://secure.ucsc.edu/s/1069/bp18/interior.aspx?sid=1069&gid=1001&pgid=780&cid=1749&dids=645"> here</a>. </p>