4daf501eaae1e56b62d212476b1a991ef592763a kate Wed Apr 1 21:30:10 2020 -0700 Finished first draft for review. refs #25217 diff --git src/hg/htdocs/covid19.html src/hg/htdocs/covid19.html index f24013c..136eb0f 100755 --- src/hg/htdocs/covid19.html +++ src/hg/htdocs/covid19.html @@ -1,112 +1,107 @@ <!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 (Updated: April 1, 2020)</h1> +<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;"> + Updated: April 1, 2020</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> +<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 UC Santa Cruz Genomics Institute are responding to the urgency of supporting biomedical research aimed at +We at the UC Santa Cruz Genomics Institute 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 SARS-Cov2 Genome Browser</a> and +the <a target="_blank" href="../cgi-bin/hgGateway?db=wuhCor1">UCSC SARS-Cov-22 Genome Browser</a> and incorporating relevant biomedical datasets such as single cell lung gene expression into the <a href="../singlecell.html">UCSC Cell Browser</a>. </p> <p> +<i> These projects are funded by generous individuals, including local donors Pat and Roland Rebele. To contribute, contact <b>TBD</b>. +</i> </p> - -<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/wuhCor1-shot.png" width=500 height=375></a> </div> - <!-- Cell browser --> <div class="col-md-6"> - <h2>UCSC Cell Browser View of Lung Gene Expression Datasets</h2> - <a href="https://cells-test.gi.ucsc.edu/?ds=eils-lung" target="_blank"> - <img src="../images/covid19/EilsLung.png" width=500 height=375></a> + <img class="text-center" alt="COVID-19 transmission as of March 13, 2020, from Nextstrain" + src="../images/covid19-transmission.mar2020.nextstrain.png" + style="margin-bottom: 5px !important"> + <div style="text-align: right; line-height: 1"> + <font SIZE=-1><em>COVID-19 transmission as of March 13, 2020</em><BR> + </font> + <font SIZE=-2> + <A HREF="https://nextstrain.org" + TARGET=_blank>Situation Report from Nextstrain.org</a> + </font> + </div> </div> </div> +<style> +img { + width: 100%; + margin: 15px 0 !important; +} +</style> -<p> <div class="row"> -<h1>Related Publications and Data Resources</h1> - <!-- Nextstrain transmission graphic --> + <!-- Genome browser --> <div class="col-md-6"> - <h2>Nextstrain Open-source Real-Time Tracking of Pathogen Evolution </h2> - <img class="text-center" alt="COVID-19 transmission as of March 13, 2020, from Nextstrain" - src="../images/covid19-transmission.mar2020.nextstrain.png" width=500 height=375> - <div style="text-align: right;"> - <FONT SIZE=-1><em>COVID-19 transmission as of March 13, 2020</em><BR> - </FONT> - <FONT SIZE=-2> - <A HREF="https://nextstrain.org" - TARGET=_blank>Situation Report from Nextstrain.org</a> - </FONT> - </div> + <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> </div> - <!-- VIPR virus cartoon --> + <!-- Cell browser --> <div class="col-md-6"> - <h2>Virus Pathogen Database and Database and Analysis Resource Center (VIPR) </h2> - <img class="text-center" alt="" - src="../images/covid19/2019_nCoV_virion_genome.png" width=500 height=375> - <div style="text-align: right;"> - <FONT SIZE=-2> - <A HREF="https://nextstrain.org" - TARGET=_blank>Viralzone 2020</a> - </FONT> - </div> + <h2>UCSC Cell Browser view of lung gene expression datasets</h2> + <a href="https://cells-test.gi.ucsc.edu/?ds=eils-lung" target="_blank"> + <img src="../images/cellBrowserAce2EilsLung.png"></a> </div> </div> -<div class="row"> - <h2>Other links</h2> + +<h2>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 Covid19 Collection</a> (all freely available) -</li> -</ul> + target="_blank">Biorxiv/Medrxiv Covid19 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> -<!-- - Nextstrain: - <a target="_blank" href="https://nextstrain.org/ncov">SARS-Cov2 browser</a> (strain tree, geographical mapping) - <p> - <p> - NCBI sequence database search, publication list, and genome display: - <a href="https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/" target="_blank"</a>NCBI Covid19 page</a> - </p> - </p> - Virus Pathogen Resource: - <a target="_blank" href="https://www.viprbrc.org/brc/home.spg?decorator=corona_ncov">VIPR Covid19 resource</a> (tools for sequence and structure analysis, comparative genomics and phenotype studies) - </p> +<li> Nextstrain open-source tracking of pathogen evolution: + <a target="_blank" href="https://nextstrain.org/ncov">SARS-Cov2 browser</a> (strain tree, geographical mapping)</li> +<li> NCBI sequence database search, publication list, and genome display: + <a href="https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/" target="_blank"</a>NCBI Covid19 page</a></li> +<li>Virus Pathogen Resource: + <a target="_blank" href="https://www.viprbrc.org/brc/home.spg?decorator=corona_ncov">VIPR Covid19 resource</a> (tools for sequence and structure analysis, comparative genomics and phenotype studies)</li> - </div> ---> +<li>CDC: <a target="_blank" href="https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/cases-in-us.html">Cases in U.S.</a>, updated at noon Mondays through Fridays</li> -</div> -</p> +<li>Johns Hopkins University: <a target="_blank" href="https://coronavirus.jhu.edu/map.html"> +Coronavirus Resource Center</a></li> + +<li>Wikipedia: <a target="_blank" href="https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2">Severe acute respiratory syndrome coronavirus 2</a></li> + +</ul> <!--#include virtual="$ROOT/inc/gbPageEnd.html"-->