ba9090c1767c6cab887fba49b2439f7cabc74e99 gperez2 Tue Nov 1 17:50:58 2022 -0700 Code review edits and updates for the public hub guidelines page, refs #28424 diff --git src/hg/htdocs/training/index.html src/hg/htdocs/training/index.html index 9eb5dc6..2d7dd14 100755 --- src/hg/htdocs/training/index.html +++ src/hg/htdocs/training/index.html @@ -1,363 +1,364 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser Training" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Getting Help with the UCSC Genome Browser</h1> <h2>Teaching with the Genome Browser</h2> <p> <font color=red><b>NEW:</b></font> Visit our <a href = "education">Education Page</a> for examples of using the Browser to teach selected topics in Molecular Biology, Genetics, Medicine, Population Biology and Evolution. </p> <hr> <div class="warn-note" style="border:2px solid #9e5900;padding:5px 20px;background-color:#e8ebf7;"> <p> <span style="font-weight:bold;color:#c70000;"> <strong><a href="mailto:genome-www@soe.ucsc.edu" target="_blank">Contact us</a> to host a Genome Browser Workshop!</strong> <a href="trainingMap.html">Map</a></span></p> <p> <b>Now taking reservations for face-to-face workshops in the US and abroad</b> ! </p> <p> Do you suspect that there is a lot more to the Genome Browser than you have been using? Timeslots are available to host a Genome Browser workshop at your institution. Thanks to the funding support of NHGRI, we are able to offer hands-on Genome Browser training onsite at your institution at very affordable prices, tailored to your audience's level of expertise. </p> <p> For more information or to submit a request to host a workshop, please <strong><a href="mailto:genome-www@soe.ucsc.edu" target="_blank">contact us</a>.</p> <p><span style="font-weight:bold;color:#c70000;"> <strong>Can't host?</strong></span> Catch one of our training sessions in your area:</p> <!--#include virtual="upcoming.html"--> </div> <h2>Online training and tutorials</h2> <p> Our video tutorials address some common questions we've gathered from our <a href = "../contacts.html#queries" target = "_blank">mailing list</a>. Along the way we try to show you interesting features of the Browser you may not have found on your own. </p> <p> Visit our <a href="https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" target="_blank" style="background-color:yellow;"> YouTube channel</a> or use the links below. </p> <!-- Left column of vids --> <!-- # this div tag indents, but I don't want it to!!!! --> <div class="row"> <div class="col-md-6"> <h2 id="videos" style="background-color:#dde6ee; color:black;"> Video tutorials </h2> <ul> <li> Browser Basics, Part One: <a class="toc" href="https://www.youtube.com/watch?v=NBDMNv2KFik&feature=youtu.be&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank> Getting around in the Browser</a>. [<a href = "vids/transcript17.pdf" target = _blank>transcript</a>]</li> <li> Browser Basics, Part Two: <a class="toc" href="https://www.youtube.com/watch?v=cYys5iXN0NY&feature=youtu.be&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank> Configuring the Browser</a>. [<a href = "vids/transcript18.pdf" target = _blank>transcript</a>]</li> <li> Browser Basics, Part Three: <a class="toc" href="https://www.youtube.com/watch?v=I25Q136d6NU&feature=youtu.be&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank> Configuration + DNA navigation</a>. [<a href = "vids/transcript19.pdf" target = _blank>transcript</a>]</li> <li> Making Links, Part One: <a class="toc" href="https://www.youtube.com/watch?v=p6TPvHDmpJk&feature=youtu.be&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank>Understanding the URL</a>. [<a href = "vids/transcript21.pdf" target = _blank>transcript</a>]</li> <li> Making Links, Part Two: <a class="toc" href="https://www.youtube.com/watch?v=xmcyz2GyRKA&feature=youtu.be&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank>Jump into genes</a>. [<a href = "vids/transcript22.pdf" target = _blank>transcript</a>]</li> <li> <!-- <img class="gbsInlineImg" style="border:0px" src="../images/new.jpg" alt="new icon"> --> Making Links, Part Three: <a class="toc" href="https://www.youtube.com/watch?v=Yy4UmepYs2Q&feature=youtu.be&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank>Composites, custom tracks, spreadsheets</a>. [<a href = "vids/transcript23.pdf" target = _blank>transcript</a>]</li> <li> Coronavirus Basics: <a class="toc" href="https://www.youtube.com/watch?v=Ee6h0xyZDOM&feature=youtu.be&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank> Coronavirus Browser SARS-CoV-2</a>. [<a href = "vids/transcript20.pdf" target = _blank>transcript</a>]</li> <li> <a class="toc" href="https://www.youtube.com/watch?v=d5rHBLXwraM&feature=youtu.be&feature=player_detailpage&v=8ATcoDTOc0g&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank>Saving and sharing sessions</a> in the Browser. [<a href = "vids/transcript16.pdf" target = _blank>transcript</a>]</li> <li> <a class="toc" href="https://www.youtube.com/watch?v=jKix2B3hwnw&feature=youtu.be&feature=player_detailpage&v=8ATcoDTOc0g&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank>Controlling visibility of data tracks</a> in the Browser. [<a href = "vids/transcript15.pdf" target = _blank>transcript</a>]</li> <li> Using the isPCR tool (<a class="toc" href="https://youtu.be/U8_QYwmdGYU?feature=player_detailpage&v=8ATcoDTOc0g&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank>isPCR</a>) in the UCSC Genome Browser. [<a href = "vids/transcript14.pdf" target = _blank>transcript</a>]</li> <li> <a class="toc" href="https://youtu.be/d4XrkjnydN8?feature=player_detailpage&v=8ATcoDTOc0g&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank>dbSNP resources</a> in the UCSC Genome Browser database. [<a href = "vids/transcript13.pdf" target = _blank>transcript</a>]</li> <li> Using the UCSC Genome Browser <a class="toc" href="https://www.youtube.com/watch?feature=player_detailpage&v=8ATcoDTOc0g&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank>Data Integrator</a>. [<a href = "vids/transcript12.pdf" target = _blank>transcript</a>]</li> </ul> </div> <!-- Right column of vids --> <div class="col-md-6" style="padding-left: 0px;"> <h2 style="background-color:#dde6ee; color:black"> Video tutorials </h2> <ul> <li> Finding a <a href="https://www.youtube.com/watch?feature=player_detailpage&v=RjB_N1GpT0U&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">list of genes</a> in a region. [<a href = "vids/transcript01.pdf" target = _blank>transcript</a>]</li> <li> Finding <a href = "https://www.youtube.com/watch?v=gK8B6sjzhmM&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">exon numbers</a>. [<a href = "vids/transcript02.pdf" target = _blank>transcript</a>]</li> <li> Finding all <a href = "https://www.youtube.com/watch?v=Y_cQ3JkhsUQ&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">SNPs in a gene</a>. [<a href = "vids/transcript03.pdf" target = _blank>transcript</a>]</li> <li> Finding <a href = "https://www.youtube.com/watch?v=ZqxlBF3vqhY&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">SNPs upstream</a> from a gene. [<a href = "vids/transcript04.pdf" target = _blank>transcript</a>]</li> <li> Find <a href = "https://www.youtube.com/watch?v=RQZ4EeYS6Zk&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">which tables belong to a data track</a>. [<a href = "vids/transcript06.pdf" target = _blank>transcript</a>]</li> <li> Identifying <a href="https://www.youtube.com/watch?v=bLnfD799AZw&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">codon numbers</a> in a gene. [<a href = "vids/transcript07.pdf" target = _blank>transcript</a>]</li> <li> Obtaining <a href="https://www.youtube.com/watch?v=6JoUqM1iKxQ&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">exon coordinates and sequences</a>. [<a href = "vids/transcript08.pdf" target = _blank>transcript</a>]</li> <li> Multi-Region View: <a href="https://www.youtube.com/watch?v=mNEJBOkf_Gk&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">Exon-only</a> display mode. [<a href = "vids/transcript09.pdf" target = _blank>transcript</a>]</li> <li> Multi-Region View: <a href="https://www.youtube.com/watch?v=0lKYdqQus0I&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank"> Alternate haplotypes</a>. [<a href = "vids/transcript10.pdf" target = _blank>transcript</a>]</li> <li> Multi-Region View:<A HREF="https://www.youtube.com/watch?v=ht4sGj1Tlxw&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank"> Discontinuous regions</a>. [<a href = "vids/transcript11.pdf" target = _blank>transcript</a>]</li> <li> How-to: Genome Browser <A HREF="https://youtu.be/dcJERBVnjio" target="_blank">in the Cloud</a>.</li> <li> How-to: Genome Browser <A HREF="https://www.youtube.com/watch?v=5zc9sqd4SD4&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">Gateway</a>.</li> <br> </ul> </div> </div> <div class="col-md-12" style="padding-left: 0px;"> <h3>Other content produced at UCSC</h3> <ul> <li> See a collection of interesting Browser views in our <a href="../goldenPath/help/sessions.html#Gallery">Session Gallery</a></li> <li> Nature: <a href="http://www.nature.com/scitable/ebooks/guide-to-the-ucsc-genome-browser-16569863" target="_blank">Guide to the UCSC Genome Browser</a></li> <li> <a href="ucscGeneFishing.pdf" target="_blank">Fishing for genes in the UCSC Browser (pdf)</a></li> <li> <a href="http://bib.oxfordjournals.org/content/14/2/144.full" target="_blank">The UCSC genome browser and associated tools</a></li> <li> <a href="https://www.ncbi.nlm.nih.gov/pubmed/18514479" target="_blank">UCSC genome browser tutorial</a></li> <li> <a href="ashg2009" >Step-by-step tutorial presented at ASHG 2009 annual meeting</a> - basic browser navigation and functionality in the context of interpreting clinical genetics reports.</li> <li> <a href="http://genomewiki.ucsc.edu/index.php/ABRF2010_Tutorial">Step-by-step tutorial presented at ABRF 2010 annual meeting</A> - how to convert files and display high-throughput sequencing results.</li> <li> <a href="ashg2014">Step-by-step tutorial presented at ASHG 2014 annual meeting</a> - includes Custom Tracks and Table Browser queries with and without filters.</li> </ul> </div> <h3>External resources</h3> <ul> <li> <a href="http://www.lifescied.org/cgi/content/full/9/2/98" target=_blank>Teaching bioinformatics and neuroinformatics by using free web-based tools</a> - student-level tutorial that demonstrates the combined use of several major bioinformatic tools (including the UCSC Genome Browser) in answering a series of related research questions</li> </ul> <h2 id="guides">User's guides for tools in the Genome Browser</h2> <div class="row"> <div class="col-md-6"> <ul> <li><a href="../goldenPath/help/hgTracksHelp.html">Genome Browser</a></li> <li><a href="../goldenPath/help/hgTracksHelp.html#CustomTracks">Custom Tracks</a></li> <li><a href="../goldenPath/help/hgTrackHubHelp.html">Track Hubs</a></li> <li><a href="../goldenPath/help/hgSessionHelp.html">Sessions</a></li> <li><a href="../goldenPath/help/hgTablesHelp.html">Table Browser</a></li> <li><a href="../goldenPath/help/hgIntegratorHelp.html">Data Integrator</a></li> </ul> </div> <!-- end column --> <div class="col-md-6"> <ul> <li><a href="../goldenPath/help/hgGeneGraph.html">Gene and Pathways Interactions</a></li> <li><a href="../cgi-bin/hgVai#intro">Variant Annotation Integrator</a></li> <li><a href="../goldenPath/help/hgGenomeHelp.html">Genome Graphs</a></li> <li><a href="../goldenPath/help/hgNearHelp.html">Gene Sorter</a></li> <li><a href="../goldenPath/help/gbib.html">Genome Browser in a Box (GBiB)</a></li> <li><a href="../goldenPath/help/gbic.html">Genome Browser in the Cloud (GBiC)</a></li> </ul> </div> <!-- end column --> </div> <!-- end row --> <h2 id="contact">Contact and mailing list information</h2> <ul> <li> <a href="../contacts.html">Genome Browser contact information</a></li> <li> <a href="http://groups.google.com/a/soe.ucsc.edu/group/genome?hl=en">Genome Browser mailing list</a> (searchable interactive discussion forum)</li> <li> <a href="../FAQ">Genome Browser FAQs</a></li> </ul> <h2>Mirroring and source code</h2> <ul> <li> <a href="../mirror.html">Genome Browser mirror sites</a></li> <li> <a href="../FAQ/FAQlicense.html#license3">Obtaining the Genome Browser source code</a></li> </ul> <h2>Associated publications and announcements</h2> <ul> <li> <a href="../goldenPath/pubs.html">Selected Genome Browser publications</a> <li> <a href="../goldenPath/newsarch.html">Genome Browser news archives</a> </ul> <h2 id="guides2">Help pages for selected parts of the Genome Browser</h2> <div class="row"> <div class="col-md-3"> <ul> <li><a href="../goldenPath/help/query.html">Querying the Genome Browser</a></li> <li><a href="../goldenPath/help/hgWiggleTrackHelp.html">Configuring graph-based tracks</a></li> <li><a href="../goldenPath/help/multiView.html">Configuring Subtracks</a></li> <li><a href="../goldenPath/help/hgBamTrackHelp.html">Configuring BAM tracks</a></li> <li><a href="../goldenPath/help/hgVcfTrackHelp.html">Configuring VCF tracks</a></li> <li><a href="../goldenPath/help/hgHicTrackHelp.html">Configuring Hi-C heatmaps</a></li> <li><a href="../goldenPath/help/hgBaseLabel.html">Base Coloring for Alignment Tracks</a></li> <li><a href="../goldenPath/help/hgCodonColoring.html">Codon Coloring for Gene Tracks</a></li> <li><a href="../goldenPath/help/hgCodonColoringMrna.html">Codon and Base Coloring for Alignments</a></li> </ul> </div> <!-- end column --> <div class="col-md-3"> <ul> <li><a href="../goldenPath/help/trackSearch.html">Track Search</a></li> <li><a href="../goldenPath/help/fileSearch.html">File Search</a></li> <li><a href="../goldenPath/help/mysql.html">MySQL access</a></li> <li><a href="../goldenPath/help/multiRegionHelp.html">Multi-Region Display</a></li> <li><a href="../goldenPath/help/liftOver.html">LiftOver tracks</a></li> <li><a href="../goldenPath/help/iupac.html">IUPAC codes</a></li> <li><a href="../goldenPath/help/genomeEuro.html">Asia and Euro Mirror</a></li> <li><a href="../goldenPath/help/mirror.html">Overview: Browser Mirror Installation</a></li> <li><a href="../goldenPath/help/mirrorManual.html">Manual: Browser Mirror Installation</a></li> </ul> </div> <!-- end column --> <div class="col-md-3"> <ul> <li><a href="../goldenPath/help/trackDb/trackDbHub.html">Track Hub Database Definitions</a></li> + <li><a href="../goldenPath/help/publicHubGuidelines.html">Public Hub Guidelines</a></li> <li><a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs">Assembly Hub Wiki</a></li> <li><a href="../goldenPath/help/twoBit.html">TwoBit Sequence Archives</a></li> <li><a href="../goldenPath/help/trix.html">Building Trix Indices</a></li> <li><a href="../goldenPath/help/haplotypes.html">Gene Haplotype Alleles</a></li> <li><a href="../goldenPath/help/hgRegMotifHelp.html">Motif Display Help Page</a></li> <li><a href="../goldenPath/help/hgIndelDisplay.html">Alignment Insertion/Deletion Display</a></li> <li><a href="../FAQ/FAQformat.html">Data Formats Page</a></li> </ul> </div> <!-- end column --> </div> <!-- end row --> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->