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{%extends "base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%block title%}Home{%endblock%}
{%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>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 — 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. …</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 –
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 …</p>
<h2>Phenotype Data</h2>
<p class="text-danger">
<span class="glyphicon glyphicon-exclamation-sign"></span>
<strong>TODO</strong>: Document this …</p>
<h2>Individual Data</h2>
<p class="text-danger">
<span class="glyphicon glyphicon-exclamation-sign"></span>
<strong>TODO</strong>: Document this …</p>
<h2>RNA-Seq Data</h2>
<p class="text-danger">
<span class="glyphicon glyphicon-exclamation-sign"></span>
<strong>TODO</strong>: Document this …</p>
</div>
</div>
{%endblock%}
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