10cd6287a3c4534b8bd7fa6d9bf649b5bbfd316b kate Mon Jun 1 08:17:23 2020 -0700 Add news item for GENCODE COVID-19 gene annotation public hub. refs #25217 diff --git src/hg/htdocs/covid19.html src/hg/htdocs/covid19.html index ab33612..3ec3962 100755 --- src/hg/htdocs/covid19.html +++ src/hg/htdocs/covid19.html @@ -1,190 +1,196 @@ <!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> <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 <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> </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> <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>UCSC Cell Browser view of lung gene expression datasets</h2> <a href="https://cells.ucsc.edu/?bp=lung" target="_blank"> <img src="../images/cellBrowserAce2EilsLung.png"></a> </div> </div> +<h2 id="news">News</h2> +<ul> +<li>May 29, 2020: Release of 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>. +View in <a target="_blank" +href="https://genome-test.gi.ucsc.edu/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> 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: <a target="_blank" href="https://bigd.big.ac.cn/ncov?lang=en"> 2019 Novel Coronavirus Resource</a> </li> <li> CDC <a target="_blank" href="https://github.com/CDCgov/SARS-CoV-2_Sequencing"> SARS-CoV-2 Sequencing Resources</a> on GitHub </li> <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 SARS-CoV-2 Sequences</a></li> <li>Virus Pathogen Resource: <a target="_blank" href="https://www.viprbrc.org/brc/home.spg?decorator=corona_ncov">VIPR SARS-CoV-2 resource</a> (tools for sequence and structure analysis, comparative genomics and phenotype studies)</li> <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 daily. </li> <li>CDC data as <a href = "https://bit.ly/coronaPerCapita" target = _blank><em>per capita</em> map</a> of the states. </li> <li>Johns Hopkins University: <a target="_blank" href="https://coronavirus.jhu.edu/map.html"> Coronavirus Resource Center</a></li> <li> CitizenScience.org: <a target="_blank" href="https://www.citizenscience.org/covid-19/" > COVID-19 citizen science and crowdsourcing projects</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> <li> Nature News graphical guide to vaccine designs: <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="news">News</h2> -<ul> -<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="funding">Funding</h2> <p> The <a target="_blank" href="https://genome.ucsc.edu"> 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> <!--#include virtual="$ROOT/inc/gbPageEnd.html"-->