{% extends 'base.html' %}

{% block head %}
<title>Home | SPIRAL</title>
{% endblock %}

{% block content %}
<center><h1 style="font-family:georgia">Welcome to SPIRAL</h1></center>
<p>SPIRAL is an algorithm that relies on a Gaussian statistical model to produce a comprehensive overview of significant
    processes in single cell RNA-seq, spatial transcriptomics or bulk RNA-seq. SPIRAL detects biological processes by
    identifying the subset of genes involved and the subset of cells, spots or samples. </p>

<br><hr><br>
<u><h2 style="font-size:1.6vw; font-family:georgia">SPIRAL output for different data sets</h2></u>

<div class="posts">
    <article>
        <a href="#" class="image"><img src={{ Wagner2018_pic }} alt="" width="200"
     height="200" onclick="window.location.href='{{ Wagner2018_link }}';"/></a>
        <h3>Single cell RNA-seq data set of Zebrafish differentiation at 7 time points</h3>
        <p><a target="_blank"
              href="https://www.science.org/doi/full/10.1126/science.aar4362">link to paper</a></p>
        <div class="container">
          <div class="horizontal-center">
            <button class="button button1" onclick="window.location.href='{{ Wagner2018_link }}';">SPIRAL results panel</button>
          </div>
        </div>
    </article>
    <article>
        <a href="#" class="image"><img src={{ MouseSP2_pic }} alt="" width="200"
     height="200" onclick="window.location.href='{{ MouseSP2_link }}';"/></a>
        <h3>Spatial transcriptomics data of a sagittal-posterior section of a mouse brain</h3>
        <p><a target="_blank"
              href="https://www.10xgenomics.com/resources/datasets/mouse-brain-serial-section-2-sagittal-posterior-1-standard-1-1-0">link to data</a></p>
        <div class="container">
          <div class="horizontal-center">
            <button class="button button1" onclick="window.location.href='{{ MouseSP2_link }}';">SPIRAL results panel</button>
          </div>
        </div>
    </article>
    <article>
        <a href="#" class="image"><img src={{ post_xenium_mouse_brain_pic }} alt="" width="200"
     height="200" onclick="window.location.href='{{ post_xenium_mouse_brain_link }}';"/></a>
        <h3>Spatial gene expression data set of a mouse brain</h3>
        <p>Visium CytAssist Gene Expression Libraries of Post-Xenium Mouse Brain (FF)</p>
        <p><a target="_blank"
              href="https://www.10xgenomics.com/datasets/visium-cytassist-gene-expression-libraries-of-post-xenium-mouse-brain-ff-using-the-mouse-whole-transcriptome-probe-set-2-standard">link to data</a></p>
        <div class="container">
          <div class="horizontal-center">
            <button class="button button1" onclick="window.location.href='{{ post_xenium_mouse_brain_link }}';">SPIRAL results panel</button>
          </div>
        </div>
    </article>
    <article>
        <a href="#" class="image"><img src={{ yaellab_differentiation_pic }} alt="" width="200"
     height="200" onclick="window.location.href='{{ yaellab_differentiation_link }}';"/></a>
        <h3>Bulk RNA-seq data of human differentiation</h3>
        <p>Samples were taken at days 0 and 7−21</p>
        <p><a target="_blank"
              href="https://zenodo.org/records/8009633">link to data</a></p>
        <div class="container">
          <div class="horizontal-center">
            <button class="button button1" onclick="window.location.href='{{ yaellab_differentiation_link }}';">SPIRAL results panel</button>
          </div>
        </div>
    </article>
    <article>
        <a href="#" class="image"><img src={{ Zhang2019_pic }} alt="" width="200"
     height="200" onclick="window.location.href='{{ Zhang2019_link }}';"/></a>
        <h3>Single cell RNA-seq data set of lymphoblastoid cells</h3>
        <p><a target="_blank"
              href="https://www.sciencedirect.com/science/article/pii/S1097276518308803?via%3Dihub">link to paper</a></p>
        <div class="container">
          <div class="horizontal-center">
            <button class="button button1" onclick="window.location.href='{{ Zhang2019_link }}';">SPIRAL results panel</button>
          </div>
        </div>
    </article>
    <article>
        <a href="#" class="image"><img src={{ normal_prostate_pic }} alt="" width="200"
     height="200" onclick="window.location.href='{{ normal_prostate_link }}';"/></a>
        <h3>Spatial transcriptomics data of a normal human prostate</h3>
        <p><a target="_blank"
              href="https://www.10xgenomics.com/datasets/normal-human-prostate-ffpe-1-standard-1-3-0">link to data</a></p>
        <div class="container">
          <div class="horizontal-center">
            <button class="button button1" onclick="window.location.href='{{ normal_prostate_link }}';">SPIRAL results panel</button>
          </div>
        </div>
    </article>
    <article>
        <a href="#" class="image"><img src={{ bulk_mouse_Bcells_pic }} alt="" width="200"
     height="200" onclick="window.location.href='{{ bulk_mouse_Bcells_link }}';"/></a>
        <h3>Bulk RNA-seq data of mouse B-cells that were treated with anti-IgM mAb</h3>
        <p>25 time points in the 6 hours post stimulation</p>
        <p><a target="_blank"
              href="https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.13757">link to paper</a></p>
        <div class="container">
          <div class="horizontal-center">
            <button class="button button1" onclick="window.location.href='{{ bulk_mouse_Bcells_link }}';">SPIRAL results panel</button>
          </div>
        </div>
    </article>
    <article>
        <a href="#" class="image"><img src={{ visium_human_colon_cancer_pic }} alt="" width="200"
     height="200" onclick="window.location.href='{{ visium_human_colon_cancer_link }}';"/></a>
        <h3>Spatial gene expression data set of human colon cancer</h3>
        <p>Visium CytAssist Gene Expression Libraries of Post-Xenium Human Colon Cancer (FFPE)</p>
        <p><a target="_blank"
              href="https://www.10xgenomics.com/datasets/visium-cytassist-gene-expression-libraries-of-post-xenium-human-colon-cancer-ffpe-using-the-human-whole-transcriptome-probe-set-2-standard">link to data</a></p>
        <div class="container">
          <div class="horizontal-center">
            <button class="button button1" onclick="window.location.href='{{ visium_human_colon_cancer_link }}';">SPIRAL results panel</button>
          </div>
        </div>
    </article>
    <article>
        <a href="#" class="image"><img src={{ arapidopsis_Ryu2019_pic }} alt="" width="200"
     height="200" onclick="window.location.href='{{ arapidopsis_Ryu2019_link }}';"/></a>
        <h3>Single cell RNA-seq data set of Arapidopsis root</h3>
        <p><a target="_blank"
              href="https://academic.oup.com/plphys/article/179/4/1444/6116601?login=false#236559283">link to paper</a></p>
        <div class="container">
          <div class="horizontal-center">
            <button class="button button1" onclick="window.location.href='{{ arapidopsis_Ryu2019_link }}';">SPIRAL results panel</button>
          </div>
        </div>
    </article>
    <article>
        <a href="#" class="image"><img src={{ aging_drosophila_brain_pic }} alt="" width="200"
     height="200" onclick="window.location.href='{{ aging_drosophila_brain_link }}';"/></a>
        <h3>Single cell RNA-seq data set of aging Drosophila brain</h3>
        <p><a target="_blank"
              href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086935/">link to paper</a></p>
        <div class="container">
          <div class="horizontal-center">
            <button class="button button1" onclick="window.location.href='{{ aging_drosophila_brain_link }}';">SPIRAL results panel</button>
          </div>
        </div>
    </article>
</div>


<! –– The "Run SPIRAL" button is no longer necessary because users do not run SPIRAL on their data through the website  ––>
{#
<div class="container">
    <form method="POST" action="/run_SPIRAL_step1">
        <div class="form-row">
            <div class="form-group">
                <center>{{ form.submit(class="btn btn-primary")}}</center>
            </div>
        </div>
    </form>
</div>
#}

<br><hr><br>
<u><h2 style="font-size:1.6vw; font-family:georgia">How to use SPIRAL?</h2></u>
<div class="formdesign">
    <div class="container">
        <div class="column">
            <div class="col-xs-11 col-sm-5 col-lg-5 center-block">
                <form method="POST" action="" onsubmit="loading();">
                    {{ form.hidden_tag() }}
                    <div class="form-vertical">
                        <div class="form-group">
                            {{ form.csrf_token() }}
                            {{ form.run(class="btn btn-primary btn-lg")}}
                            <text>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</text>
                            {{ form.csrf_token() }}
                            {{ form.view(class="btn btn-primary btn-lg")}}
                        </div>
                    </div>
                </form>
            </div>
        </div>
    </div>
</div>


<br><hr><br>
<u><h2 style="font-size:1.6vw; font-family:georgia">How to cite?</h2></u>
<p style="font-size:15px">Biran, Hadas, Tamar Hashimshony, Tamar Lahav, Or Efrat, Yael Mandel-Gutfreund, and Zohar Yakhini. "Detecting significant expression patterns in single-cell and spatial transcriptomics with a flexible computational approach." Scientific Reports 14, no. 1 (2024): 26121.</p>
<div style="text-align: right;"><img src="/static/Technion_logo.jpg" width="100" height="40" alt="Technion logo"></div>

<p style="font-size:11px">Some elements in this website were designed by <a href="https://html5up.net">HTML5 UP</a>.</p>
{% endblock %}