1 files changed, 88 insertions, 8 deletions
diff --git a/uploader/templates/index.html b/uploader/templates/index.html
index e3f5af4..aa1414e 100644
--- a/uploader/templates/index.html
+++ b/uploader/templates/index.html
@@ -5,23 +5,103 @@
 
 {%block pagetitle%}Home{%endblock%}
 
-{%block breadcrumb%}
-<li class="breadcrumb-item active">
-  <a href="{{url_for('base.index')}}">Home</a>
-</li>
-{%endblock%}
-
 {%block contents%}
 
 <div class="row">
   {{flash_all_messages()}}
   <div class="explainer">
-    <p>Welcome to the <strong>GeneNetwork Data Quality Control and Upload System</strong>. This system is provided to help in uploading your data onto GeneNetwork where you can do analysis on it.</p>
+    <p>Welcome to the <strong>GeneNetwork Data Upload and Quality Control
+        System</strong>.</p>
+    <p>This tool helps you prepare and upload research data to GeneNetwork for
+      analysis.</p>
 
-    <p>Click on the menu items on the left to select the kind of data you want to upload.</p>
+    <h2 class="heading">Getting Started</h2>
+    <p>The sections below explain the features of the system. Review this guide
+      to learn how to use the system.</p>
 
     {%block extrapageinfo%}{%endblock%}
+
+    <h3 class="subheading">Species</h3>
+
+    <p>GeneNetwork supports genetic studies across multiple species (e.g. mice
+      [Mus musculus], human [homo sapiens], rats [Rattus norvegicus], etc.) .
+      Here you can:</p>
+    <ul>
+      <li>View all species that are currently supported</li>
+      <li>Add new species not yet in the system</li>
+    </ul>
+
+    <h3 class="subheading">Populations</h3>
+
+    <p>A "population" refers to a specific subgroup within a species that you’re
+      studying (e.g., BXD mice). Here you can:</p>
+    <ul>
+      <li>View the populations that exist for a selected species</li>
+      <li>Add new populations of study for a selected species</li>
+    </ul>
+
+    <h3 class="subheading">Samples</h3>
+
+    <p>Manage individual specimens or cases used in your experiments. These
+      include:</p>
+
+    <ul>
+      <li>Experimental subjects</li>
+      <li>Data sources (e.g., tissue samples, clinical cases)</li>
+      <li>Strain means (instead of entering multiple BXD1 individuals, for
+        example, the mean would be entered for a single BXD1 strain)</li>
+    </ul>
+
+
+    <h3 class="subheading">Genotype Data</h3>
+
+    <p>Upload and review genetic markers and allele encodings for your
+      population. Key details:</p>
+
+    <ul>
+      <li>Markers are species-level (e.g., mouse SNP databases).</li>
+      <li>Allele data is population-specific (tied to your experimental
+        samples).</li>
+    </ul>
+
+    <p><strong>Requirement</strong>: Samples must already have been registered
+      in the system before uploading genotype data.</p>
+
+    <h3 class="subheading">Phenotype Data</h3>
+
+    <p>Phenotypes are the visible traits or features of a living thing. For
+      example, phenotypes include:</p>
+
+    <ul>
+      <li>Weight</li>
+      <li>Height</li>
+      <li>Color (such as the color of fur or eyes)</li>
+    </ul>
+
+    <p>This part of the system will allow you to upload and manage the values
+      for different phenotypes from various samples in your studies.</p>
+
+    <!--
+
+        <h3 class="subheading">Expression Data</h3>
+
+    <p class="text-danger">
+      <span class="glyphicon glyphicon-exclamation-sign"></span>
+      <strong>TODO</strong>: Document this &hellip;</p>
+
+    <h3 class="subheading">Individual Data</h3>
+
+    <p class="text-danger">
+      <span class="glyphicon glyphicon-exclamation-sign"></span>
+      <strong>TODO</strong>: Document this &hellip;</p>
+
+    <h3 class="subheading">RNA-Seq Data</h3>
+
+    <p class="text-danger">
+      <span class="glyphicon glyphicon-exclamation-sign"></span>
+      <strong>TODO</strong>: Document this &hellip;</p>
   </div>
+  -->
 </div>
 
 {%endblock%}