de306bc0c8046b618da4950018406bdbe4b2ff21 kate Tue Sep 8 16:25:54 2020 -0700 Update COVID-19 landing page News section and add GSAID terms and conditions. Ahead of UCSC SARS-CoV-2 manuscript release in Nature Genetics. refs #26195 diff --git src/hg/htdocs/covid19.html src/hg/htdocs/covid19.html index ae3d1e0..b9eb014 100755 --- src/hg/htdocs/covid19.html +++ src/hg/htdocs/covid19.html @@ -1,52 +1,51 @@ <!DOCTYPE html> <!--#set var="TITLE" value="COVID-19 Resources at UCSC" --> <!--#set var="ROOT" value="." --> <!--#include virtual="$ROOT/inc/gbPageStart.html"--> <h1>COVID-19 Pandemic Resources at UCSC <span bgcolor=#f3e0be><font color=#555 size=-1 style="background-color: #f3e0be; padding-left: 10px; padding-right: 10px; margin-left: 15px;"> - <a href="#news">Updated: June 1, 2020</a></font></span></h1> + <a href="#news">Updated: September 8, 2020</a></font></span></h1> <div class="row"> <div class="col-md-6"> <p> The SARS-CoV-2 coronavirus emerged in December 2019 as a novel human pathogen causing a severe acute respiratory syndrome (COVID-19). In the following months, the disease spread internationally and was <A TARGET="_BLANK" HREF="https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---11-march-2020"> declared a pandemic by the World Health Organization</a> on March 11, 2020. </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 therapeutics and a vaccine for this devastating illness by fast-tracking the <a target="_blank" href="../cgi-bin/hgGateway?db=wuhCor1">UCSC Genome Browser for SARS-Cov-2</a> and incorporating relevant biomedical datasets such as single-cell lung gene expression into the <a target="_blank" href="../singlecell.html">UCSC Cell Browser</a>. A manuscript describing this work, <a target="_blank" href="https://www.biorxiv.org/content/10.1101/2020.05.04.075945v1"> The UCSC SARS-CoV-2 Genome Browser</a>, -is available from the +is <i>in press</i> and currently available from the <a target="_blank" href="https://biorxiv.org">bioRxiv</a> preprint server. </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" 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> @@ -84,58 +83,73 @@ 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>May 29, 2020: Release of public track hub +<li> +</li> +<b>August 7, 2020</b>: +<a target="_blank" href="https://genome.ucsc.edu/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> +<b>July 7, 2020</b>: +Annotation tracks released: <a target="_blank" <a target="_blank" href="https://genome.ucsc.edu/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>. +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" > 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: <a href="https://connect.biorxiv.org/relate/content/181" target="_blank">BioRxiv/MedRxiv COVID-19 Collection</a> (all freely available)</li> <li><a target="_blank" href="https://pages.semanticscholar.org/coronavirus-research">COVID-19 Open Research Dataset</a> of scholarly literature</li> <li> GISAID <a target="_blank" href="https://gisaid.org">the main repository of SARS-CoV-2 sequences</a> +(please see GISAID's + <a target="_blank" href="https://www.gisaid.org/registration/terms-of-use/">terms and conditions</a>) </li> <li> NIH Office of Data Science Strategy <a target="_blank" href="https://datascience.nih.gov/covid-19-open-access-resources">Open-Access Data and Computational Resources to Address COVID-19</a> </li> <li> European Molecular Biology Laboratory/European Bioinformatics Institute (EMBL-EBI) and partners: <a target="_blank" href="https://www.covid19dataportal.org/"> COVID-19 Data Portal</a> </li> <li> China National Center for Bioinformation: