uploader/templates/index.html


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{%extends "base.html"%}
{%from "flash_messages.html" import flash_all_messages%}

{%block title%}Home{%endblock%}

{%block pagetitle%}Home{%endblock%}

{%block contents%}

<div class="row">
  {{flash_all_messages()}}
  <div class="explainer">
    <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>

    <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</h2>

    <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">Expression Data</h3>

    <p class="text-danger">
      <span class="glyphicon glyphicon-exclamation-sign"></span>
      <strong>TODO</strong>: Document this &hellip;</p>

    <h3 class="subheading">Phenotype 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%}