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-rw-r--r--uploader/templates/base.html4
-rw-r--r--uploader/templates/index.html80
-rw-r--r--uploader/templates/login.html2
3 files changed, 82 insertions, 4 deletions
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 3af14ef..886f503 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -48,10 +48,10 @@
title="View and manage species information.">Species</a></li>
<li><a href="{{url_for('species.populations.index')}}"
title="View and manage species populations.">Populations</a></li>
- <li><a href="{{url_for('species.populations.genotypes.index')}}"
- title="Upload Genotype data.">Genotype Data</a></li>
<li><a href="{{url_for('species.populations.samples.index')}}"
title="Upload population samples.">Samples</a></li>
+ <li><a href="{{url_for('species.populations.genotypes.index')}}"
+ title="Upload Genotype data.">Genotype Data</a></li>
<li><a href="{{url_for('expression-data.index.index')}}"
title="Upload expression data.">Expression Data</a></li>
<li><a href="#"
diff --git a/uploader/templates/index.html b/uploader/templates/index.html
index e3f5af4..0fa4a1b 100644
--- a/uploader/templates/index.html
+++ b/uploader/templates/index.html
@@ -18,9 +18,87 @@
<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>Click on the menu items on the left to select the kind of data you want to upload.</p>
+ <p>The sections below provide an overview of what features the menu items on
+ the left provide to you. Please peruse the information to get a good
+ big-picture understanding of what the system provides you and how to get
+ the most out of it.</p>
{%block extrapageinfo%}{%endblock%}
+
+ <h2>Species</h2>
+
+ <p>The GeneNetwork service provides datasets and tools for doing genetic
+ studies &mdash; from
+ <a href="{{gn2server_intro}}"
+ target="_blank"
+ title="GeneNetwork introduction — opens in a new tab.">
+ its introduction</a>:
+
+ <blockquote class="blockquote">
+ <p>GeneNetwork is a group of linked data sets and tools used to study
+ complex networks of genes, molecules, and higher order gene function
+ and phenotypes. &hellip;</p>
+ </blockquote>
+ </p>
+
+ <p>With this in mind, it follows that the data in the system is centered
+ aroud a variety of species. The <strong>species section</strong> will
+ list the currently available species in the system, and give you the
+ ability to add new ones, if the one you want to work on does not currently
+ exist on GeneNetwork</p>
+
+ <h2>Populations</h2>
+
+ <p>Your studies will probably focus on a particular subset of the entire
+ species you are interested in &ndash your population.</p>
+ <p>Populations are a way to organise the species data so as to link data to
+ specific know populations for a particular species, e.g. The BXD
+ population of mice (Mus musculus)</p>
+ <p>In older GeneNetwork documentation, you might run into the term
+ <em>InbredSet</em>. Should you run into it, it is a term that we've
+ deprecated that essentially just means the population.</p>
+
+ <h2>Samples</h2>
+
+ <p>These are the samples or individuals (sometimes cases) that were involved
+ in the experiment, and from whom the data was derived.</p>
+
+ <h2>Genotype Data</h2>
+
+ <p>This section will allow you to view and upload the genetic markers for
+ your species, and the genotype encodings used for your particular
+ population.</p>
+ <p>While, technically, genetic markers relate to the species in general, and
+ not to a particular population, the data (allele information) itself
+ relates to the particular population it was generated from &ndash;
+ specifically, to the actual individuals used in the experiment.</p>
+ <p>This is the reason why the genotype data information comes under the
+ population, and will check for the prior existence of the related
+ samples/individuals before attempting an upload of your data.</p>
+
+ <h2>Expression Data</h2>
+
+ <p class="text-danger">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ <strong>TODO</strong>: Document this &hellip;</p>
+
+ <h2>Phenotype Data</h2>
+
+ <p class="text-danger">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ <strong>TODO</strong>: Document this &hellip;</p>
+
+ <h2>Individual Data</h2>
+
+ <p class="text-danger">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ <strong>TODO</strong>: Document this &hellip;</p>
+
+ <h2>RNA-Seq Data</h2>
+
+ <p class="text-danger">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ <strong>TODO</strong>: Document this &hellip;</p>
</div>
</div>
diff --git a/uploader/templates/login.html b/uploader/templates/login.html
index bbca42f..1f71416 100644
--- a/uploader/templates/login.html
+++ b/uploader/templates/login.html
@@ -5,7 +5,7 @@
{%block pagetitle%}log in{%endblock%}
{%block extrapageinfo%}
-<p>
+<p class="text-dark text-primary">
You <strong>do need to be logged in</strong> to upload data onto this system.
Please do that by clicking the "Log In" button at the top of the page.</p>
{%endblock%}