766b5baa0dc8dfb4d0930e6c36ca29035becf364 brianlee Thu Apr 23 12:40:18 2020 -0700 Adding help pages section on training index and also putting user guides into columns diff --git src/hg/htdocs/training/index.html src/hg/htdocs/training/index.html index 42eee9c..2285890 100755 --- src/hg/htdocs/training/index.html +++ src/hg/htdocs/training/index.html @@ -302,74 +302,110 @@ </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> +<div class="row"> + <div class="col-md-6"> <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> + <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>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> + 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> +<a name="help"</a> +<h2>Various Help pages for 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">Installation of Browser mirror overivew</a></li> + <li><a href="../goldenPath/help/mirrorManual.html">Installation of Browser mirror manual</a></li> + </ul> + </div> + <div class="col-md-3"> + <ul> + <li><a href="../goldenPath/help/trackDb/trackDbHub.html">Track Hub Database Definitions</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" -->