16ab1a313abfee9a5f155ea778ba47addfc0cd81 kuhn Tue Sep 24 14:46:10 2019 -0700 added U of Oregon workshop to long list diff --git src/hg/htdocs/training/index.html src/hg/htdocs/training/index.html index 6a22274..2ae10a7 100755 --- src/hg/htdocs/training/index.html +++ src/hg/htdocs/training/index.html @@ -1,336 +1,341 @@ <!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> <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="http://bit.ly/ucscTraining" target="_blank">Host</a> a Genome Browser Workshop!</strong> <a href="trainingMap.html">Map</a></span></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. <strong><a href="http://bit.ly/ucscTraining" target="_blank">Host</a></strong> </p> <p> For more information or to submit a request to host a workshop, please visit our <a href="http://bit.ly/ucscTraining" target="_blank">sign-up page</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> <table class="gbsNoBorder"> <!-- stored for later Contact <A HREF="mailto:ucscgbtraining@soe.ucsc.edu">ucscgbtraining@soe.ucsc.edu</A> for access. --> <!-- above address is ucscgbtraining at soe.ucsc.edu --> <td>October 18, 2019</td> <td> American Society of Human Genetics (<a href = "https://www.ashg.org/2019meeting/asp/soe/webroot/soe.shtml#?search=ucsc" - TARGET = _blank>ASHG</a>). Houston TX. + TARGET = _blank>ASHG</a>). Houston, TX. </td> </tr> <tr> <td>October 21-22, 2019</td> <td> <a href = "http://mayoclinic.org" target = _blank>Mayo Clinic</a>. Rochester, MN. </td> </tr> <tr> <td>November 14, 2019</td> <td> International Society for Computational Biology (<a href = "https://www.iscb.org/iscbafrica2019-ps/iscbafrica2019-worktut#ucsc" target = _blank>ISCB</a>). Kumasi, Ghana. </td> </tr> <tr> <td>November 19-20, 2019</td> <td> <a href = "https://www.erasmusmc.nl/en" target = _blank>Erasmus University Medical Center</a>. Rotterdam, Netherlands. </td> </tr> <!-- <tr> <td>January 11-15, 2020</td> <td> <a href = "https://intlpag.org/2020/" target = _blank>Plant and Animal Genomes</a>. San Diego, CA. </td> </tr> <tr> FUTURE: --> <tr> <td> further:</td> <td> <!-- new row: <br> - --> <a href = "https://intlpag.org/2020/" target = _blank>PAG</a> | - UNC | NIEHS | Duke | OHSU | + UNC | NIEHS | Duke | + +<!-- + Genomics in Action at UofO +--> + + U Oregon | OHSU | <a href = "https://www.acmgmeeting.net/acmg2020/Public/mainhall.aspx" target = _blank>ACMG</a> San Antonio | <!-- <a href = "https://eshg.org/index.php?id=home" target = _blank>ESHG</a> Berlin --> ESHG Berlin </td> </tr> </table> </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 style="background-color:#dde6ee; color:black;"> Video tutorials </h2> <ul> <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> <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> </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> 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> <a href="https://www.youtube.com/watch?v=mNEJBOkf_Gk&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">Exon-only</a> display mode (Multi-Region View). [ <a href = "vids/transcript09.pdf" target = _blank>transcript</a> ]</li> <li> Viewing <a href="https://www.youtube.com/watch?v=0lKYdqQus0I&list=UUQnUJepyNOw0p8s2otX4RYQ" target="_blank">alternate haplotypes</a> (Multi-Region View). [ <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> in the Browser. [ <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> <a name="guides"</a> <h2>User's guides for tools in the Genome Browser</h2> <ul> <li> <a href="../goldenPath/help/hgTracksHelp.html#CustomTracks">Custom Tracks</a></li> <li> <a href="../goldenPath/help/hgTracksHelp.html#CustomTracks">Custom Tracks</a></li> <li> <a href="../goldenPath/help/hgTracksHelp.html">Genome Browser</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> <li> <a href="../cgi-bin/hgVai#intro">Variant Annotation Integrator</a></li> <li> <a href="../goldenPath/help/hgGeneGraph.html">Gene and Pathways Interactions</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> <li> <a href="../goldenPath/help/multiRegionHelp.html">Multi-Region Display</a></li> <li> <a href="../goldenPath/help/trackSearch.html">Track Search</a></li> </ul> <h2>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> (interactive discussion forum)</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> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->