a8d8d0e805bc550786aef8570670c5d16ffb65ee
mspeir
  Sun Apr 28 18:32:11 2024 -0700
updated index, added gb101.md stub, added page_template.md refs #30335

diff --git docs/gb101.md docs/gb101.md
new file mode 100644
index 0000000..c818ab4
--- /dev/null
+++ docs/gb101.md
@@ -0,0 +1,166 @@
+% Genome Browser Tutorials
+
+# Introduction to the UCSC Genome Browser
+
+This page attempts to introduce you to the basics of using the UCSC Genome Browser including:
+
+- Basic Navigation
+- Basic Table Browser Query
+- Basic BLAT Query
+
+## Sections
+
+Use the sections below to learn about the UCSC Genome Browser interface.
+
+<div class="row" style="padding-top: 15px">
+<div class="col-md-4">
+<div class="panel panel-default" style="padding-bottom: 10px">
+<h3 class="panel-title" style="width: -webkit-fill-available;"
+>Genome Browser Interface</h3>
+
+Annotated screenshot of the Genome Browser interface. Explains what all the buttons do
+
+<p style="text-align: end">
+<button>[View](#annot-screenshot)</button>
+</p>
+</div>
+</div>
+<div class="col-md-4">
+<div class="panel panel-default" style="padding-bottom: 10px">
+<h3 class="panel-title" style="width: -webkit-fill-available;"
+>Guided Workthrough</h3>
+
+Explains the basis of using/navigating the Genome Browser interface. 
+Also explains a very basic Table Browser query and BLAT query.
+
+<p style="text-align: end">
+<button>[View](#guided-work)</button>
+</p>
+</div>
+</div>
+<div class="col-md-4" style="padding-top: 15px">
+<div class="panel panel-default" style="padding-bottom: 10px">
+<h3 class="panel-title" style="width: -webkit-fill-available;"
+>Interactive Tutorial</h4>
+
+Steps you through the basic functionality in the Genome Browser itself.  
+
+
+<p style="text-align: end">
+<button>[View](../cgi-bin/hgTracks?#showTutorial)</button>
+</p>
+</div>
+</div>
+</div>
+
+## Annotated Screenshot
+
+![Annotated image of the UCSC Genome Browser Interface](../images/annot-screenshot-sarCov2.jpg)
+
+| Item | Explanation |
+|------|-------------|
+| Menu | Find BLAH   |
+
+(Wee need something below the table otherwise later markdown isn't properly interpreted)
+
+## Guided Workthorugh
+
+This walkthrough will take you through the basic Genome Browser functionality.
+
+By the end of the workthrough you should be able to do these three things:
+
+1. Naviagte the Genome Browser Interface
+2. Perform a basic Table Browser query
+3. Perform a simple BLAT query
+
+### Genome Browser Basics
+
+In this guided walkthrough, we go from selecting our genome (hg38 in this
+case), to going to our gene of interest (BLAH), to turning off and on some of
+our favorite tracks, before finally BLAH. 
+
+#### Step 1: Choose your genome
+
+<!--
+We are going to use bootstrap columns to put the image/text side by side
+Alternate the images left/right between different sections, mostly for aesthetics
+--->
+
+<div class="row">
+<div class="col-md-6">
+
+<img src="../images/GenomeSelect.jpg" alt="Genome selection" style="max-width:100%;">
+
+</div>
+<div class="col-md-6">
+
+Go to BLAH, select your genome from the diagram or search for in the search box at the top left of the screen.
+
+For this walkthrough, we will select "Human" and stick with the default GRCh38/hg38 assembly.
+</div>
+</div>
+
+<!-- note to self, something seems off with the image handling here? like too wide and not auto-fitting to the col -->
+
+#### Step 2: Navigate to your gene of interest
+
+<div class="row">
+<div class="col-md-6">
+
+After selecting a genome, enter a gene name into the search box. In our case,
+we will enter "HUNK", a gene for BLAH, into the search box. 
+
+After typing in the name, select the gene name "HUNK" from the list that
+appears below the search box. You will be taken directly to that gene location. 
+</div>
+<div class="col-md-6">
+
+<img src="../images/GeneSearch.jpg" alt="Genome selection" style="max-width:100%;">
+
+</div>
+</div>
+
+#### Step 3: Configure the Genome Browser tracks
+
+<div class="row">
+<div class="col-md-6">
+
+The horizontal lines of genomic data in the UCSC Genome Browser are known as **tracks**. they may BLAH, BLAH, and BLAH
+
+</div>
+<div class="col-md-6">
+
+<!--
+<img> here
+-->
+
+</div>
+</div>
+
+### Simple Table Browser Query
+
+#### Step 1:
+
+BLAH
+
+#### Step 2:
+
+BLAH
+
+#### Step 3:
+
+BLAH
+
+### Simple BLAT Query
+
+#### Step 1:
+
+BLAH
+
+#### Step 2:
+
+BLAH
+
+#### Step 3:
+
+BLAH