c4b68ccd0ffbb9122db69d03de0ee94dc19daaac lrnassar Wed Jun 26 14:13:08 2019 -0700 Adding new assembly papAnu4 and bosTau9 to newsArch page #20769 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 68736fb..f238329 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,33 +39,99 @@ </div> <div class="col-sm-3"> <ul> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2019 archived news ============= --> <a name="2019"></a> +<a name="062819"></a> +<h2>Jun. 28, 2019 New Genome Browsers: Cow, bosTau9 (<em>Bos taurus</em>) and +Baboon, papAnu4 (<em>Papio anubis</em>)</h2> +<p> +Genome browsers are now available for the <em>Bos taurus</em> assembly released in Apr. 2018 by the +<a href="https://www.ars.usda.gov/" target="_blank"> USDA Agricultural Research Service</a> (ARS-UCD1.2), +and the <em>Papio anubis</em> assembly released in Apr. 2017 by the +<a href="https://www.hgsc.bcm.edu/" target="_blank"> Human Genome Sequencing Center</a> (Panu_3.0). +<h3>About the assembly (bosTau9):</h3> +<ul> + <li><b>UCSC Genome Browser assembly ID:</b> <a href="../../cgi-bin/hgGateway?db=bosTau9" + target="_blank">bosTau9</a></li> + <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.ars.usda.gov/"> +USDA Agricultural Research Service</a></li> + <li><b>Assembly date:</b> Apr. 2018</li> + <li><B>Accession ID:</B> GCF_002263795.1</li> + <li><B>NCBI Genome ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/genome/82" +TARGET="_blank">82</A> (<em>Bos taurus</em>)</li> + <li><B>NCBI Assembly ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/assembly/1677391" +TARGET="_blank">1677391</A></li> + <li><B>NCBI BioProject ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/bioproject/391427" +TARGET="_blank">391427</A></li> + <li><B>NCBI BioSample ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/biosample/SAMN03145444" +TARGET="_blank">SAMN03145444</A></li> + <li><b>Scaffold count: </b>2,211</li> + <li><b>Total size: </b>2,358,151,106</li> + <li><a href="../goldenPath/credits.html#Cow_credits" +target="_blank" >Acknowledgments</a></li> +</ul> +<h3>About the assembly (papAnu4):</h3> +<ul> + <li><b>UCSC Genome Browser assembly ID:</b> <a href="../../cgi-bin/hgGateway?db=papAnu4" + target="_blank">papAnu4</a></li> + <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.hgsc.bcm.edu/"> +Human Genome Sequencing Center</a></li> + <li><b>Assembly date:</b> Apr. 2017</li> + <li><B>Accession ID:</B> GCF_000264685.3</li> + <li><B>NCBI Genome ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/genome/394" +TARGET="_blank">394</A> (<em>Papio anubis</em>)</li> + <li><B>NCBI Assembly ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/assembly/1082401" +TARGET="_blank">1082401</A></li> + <li><B>NCBI BioProject ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/bioproject/54005" +TARGET="_blank">54005</A></li> + <li><B>NCBI BioSample ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/biosample/SAMN02981400" +TARGET="_blank">SAMN02981400</A></li> + <li><b>Scaffold count: </b>71,135</li> + <li><b>Total size: </b>2,959,373,024</li> + <li><a href="../goldenPath/credits.html#Baboon_credits" +target="_blank" >Acknowledgments</a></li> +</ul> +<h3>Data and Downloads:</h3> +<ul> + <li><a href="../goldenPath/credits.html" +target="_blank" >Data use conditions and restrictions</a></li> + <li><a href="../goldenPath/help/ftp.html" +target="_blank" >Rsync</a></li> + <li>FTP: <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/" +target="_blank" >Cow</a> and +<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/papAnu4/" +target="_blank" >Baboon</a></li> + <li>Downloads page: <a href="http://hgdownload.soe.ucsc.edu/downloads.html#cow" +target="_blank" >Cow</a> and +<a href="http://hgdownload.soe.ucsc.edu/downloads.html#baboon" +target="_blank" >Baboon</li> +</ul> +</p> + <a name="062519"></a> <h2> Jun. 25, 2019 JSON API now available</h2> - <p> The UCSC Genome Browser is pleased to announce its new <a href="help/api.html" target="_blank">JavaScript Object Notation (JSON) Application Programming Interface (API)</a>. The API provides direct access to different data including annotations and sequence data for both native Genome Browser assemblies as well as hubs.</p> <p> Some functions possible with the API include: <ul> <li>List of all available UCSC Genome Browser assemblies</li> <li>List of chromosomes contained in a UCSC Genome Browser assembly or assembly hub</li> <li>List of all data tracks in a specific assembly</li> <li>Extraction of any track data from a UCSC Genome Browser assembly or hub</li> </ul></p>