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diff --git a/uploader/templates/index.html b/uploader/templates/index.html index 94060b7..aa1414e 100644 --- a/uploader/templates/index.html +++ b/uploader/templates/index.html @@ -1,84 +1,107 @@ {%extends "base.html"%} {%from "flash_messages.html" import flash_all_messages%} -{%block title%}Data Upload{%endblock%} +{%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> - <h1 class="heading">data upload</h1> + <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> - <div class="explainer"> - <p>Each of the sections below gives you a different option for data upload. - Please read the documentation for each section carefully to understand what - each section is about.</p> - </div> -</div> + {%block extrapageinfo%}{%endblock%} -<div class="row"> - <h2 class="heading">R/qtl2 Bundles</h2> + <h3 class="subheading">Species</h3> - <div class="explainer"> - <p>This feature combines and extends the two upload methods below. Instead of - uploading one item at a time, the R/qtl2 bundle you upload can contain both - the genotypes data (samples/individuals/cases and their data) and the - expression data.</p> - <p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither - of the methods below can handle.</p> - - <a href="{{url_for('upload.rqtl2.select_species')}}" - title="Upload a zip bundle of R/qtl2 files"> - <button class="btn btn-primary">upload R/qtl2 bundle</button></a> - </div> -</div> + <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> -<div class="row"> - <h2 class="heading">Expression Data</h2> + <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> - <div class="explainer"> - <p>This feature enables you to upload expression data. It expects the data to - be in <strong>tab-separated values (TSV)</strong> files. The data should be - a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a - list of the <em>phenotypes</em> and the first row is a list of - <em>samples/cases</em>.</p> - - <p>If you haven't done so please go to this page to learn the requirements for - file formats and helpful suggestions to enter your data in a fast and easy - way.</p> - - <ol> - <li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies - with our system requirements. ( - <a href="{{url_for('entry.data_review')}}#data-concerns" - title="Details for the data expectations.">Help</a> - )</li> - <li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept - <strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong> - files (<a href="{{url_for('entry.data_review')}}#file-types" - title="Details for the data expectations.">Help</a>)</li> - </ol> - </div> + <h3 class="subheading">Samples</h3> - <a href="{{url_for('entry.upload_file')}}" - title="Upload your expression data" - class="btn btn-primary">upload expression data</a> -</div> + <p>Manage individual specimens or cases used in your experiments. These + include:</p> -<div class="row"> - <h2 class="heading">samples/cases</h2> + <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> - <div class="explainer"> - <p>For the expression data above, you need the samples/cases in your file to - already exist in the GeneNetwork database. If there are any samples that do - not already exist the upload of the expression data will fail.</p> - <p>This section gives you the opportunity to upload any missing samples</p> - </div> - <a href="{{url_for('samples.select_species')}}" - title="Upload samples/cases/individuals for your data" - class="btn btn-primary">upload Samples/Cases</a> + <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 …</p> + + <h3 class="subheading">Individual Data</h3> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> + + <h3 class="subheading">RNA-Seq Data</h3> + + <p class="text-danger"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + <strong>TODO</strong>: Document this …</p> + </div> + --> </div> {%endblock%} |