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<!DOCTYPE html>
<html>
  {% include 'header.html' %}
  {% include 'mapheader.html' %}
    <body>
      {% include 'banner.html' %}
      {% include 'menu.html' %}

      <section>
                <div class="intro">

                  <p>
                    COVID-19 PubSeq is a free and open online
                    bioinformatics public sequence resource with
                    on-the-fly analysis of
                    sequenced <a href="https://pubmed.ncbi.nlm.nih.gov/?term=sars-cov-2&sort=date">SARS-CoV-2</a>
                    samples that allows for a quick turnaround in
                    identification of new virus strains. PubSeq allows
                    anyone to upload sequence material in the form of
                    FASTA or FASTQ files with accompanying metadata
                    through the <a href="/upload">web interface</a>
                    or <a href="/apidoc">REST API</a>. For more
                    information see the <a href="/about">FAQ!</a>.
                  </p>

                  <section class="flex-container">
                      <div id="map_view" class="map">
                          <div id="mapid"></div>
                      </div>

                      <div id="feed">
                          <input name="feed-tabs" type="radio" id="tab-all-items" checked/>
                          <label for="tab-all-items">All Items</label>
                          <input name="feed-tabs" type="radio" id="tab-arxiv-articles"/>
                          <label for="tab-arxiv-articles">Arxiv</label>
                          <input name="feed-tabs" type="radio" id="tab-pubmed-articles"/>
                          <label for="tab-pubmed-articles">Pubmed</label>
                          <input name="feed-tabs" type="radio" id="tab-tweets"/>
                          <label for="tab-tweets">Tweets</label>
                          <input name="feed-tabs" type="radio" id="tab-commits"/>
                          <label for="tab-commits">Commits</label>
                          <ul class="tab content-all-items">
                              <!-- Begin News -->
                                  {% if all_items %}
                                  {% for item in all_items|sort(reverse=true, attribute="score")%}
                                  <li>
                                      {% if item['authors'] %}
                                      <!-- Arxiv article -->
                                      <p>
                                          <b>[arxiv]</b>
                                          <a href="{{ item['url'] }}" target="_blank">
                                              {{item['title']}}
                                          </a>
                                          <br/>
                                          <b>Authors:</b> {{ item['authors'] }}
                                          <br/>
                                          <b>Abstract:</b> {{ item['abstract']}}...
                                          <br/>
                                          <b>Submitted:</b> {{ item['submission']}}
                                      </p>

                                      {% elif item['full-authors'] %}
                                      <!-- Pubmed Article -->
                                      <p><b>[Pubmed]:</b>
                                          <a href="https://pubmed.ncbi.nlm.nih.gov/{{ item['docsum-pmid'] }}" target="_blank"><b>Summary:</b>
                                              {{ item['summary'] }}
                                          </a> <br/>
                                          <b>Full Authors:</b> {{ item['full-authors'] }} <br/>
                                          <b>Short Authors:</b> {{ item['short-authors'] }} <br/>
                                          <b>Citation:</b> {{ item['citation'] }} <br/>
                                          <b>Short Journal Citation:</b> {{ item['short-journal-citation'] }} <br/>
                                      </p>

                                      {% elif item['tweet'] %}
                                      <!-- Tweets -->
                                      <p>
                                          <b>[Tweet]:</b>
                                          {{ item['tweet']|urlize(40, target="_blank")}}
                                          <small>
                                              <a href="{{ item['url'] }}" target="_blank">source</a></small>
                                          <br/>
                                          by {{ item['author'] }}
                                          <br/>
                                          <small>{{ item['timeposted'] }}</small>
                                      </p>

                                      {% elif item['repository-url'] %}
                                      <!-- Commits -->
                                      <p>
                                          <b>[Commit]:</b>
                                          <a href="{{ item.url }}" target="_blank">
                                              {{ item.hash.split(":")[-1][:7] }}: {{ item.content }}
                                          </a>
                                          <br/>
                                          <small>
                                              <a href="{{ item['repository-url'] }}" target="_blank"> {{ item.author }}/{{ item.repository }}</a>
                                              on {{ item.timeposted }}
                                          </small>
                                      </p>
                                      {% endif %}
                                  </li>
                                  {%endfor%}

                                  {% else %}
                                  There are no items to display :(
                                  {% endif %}
                              <!-- End News -->
                          </ul>
                          <ul class="tab content-arxiv-articles">
                              {% if arxiv_articles %}
                              {% for article in arxiv_articles|sort(reverse=true, attribute="score")%}
                              <li>
                                  <p><a href="{{article['url']}}">{{ article['title'] }}</a></p>
                                  <p><b>Authors:</b> {{ article['authors'] }}</p>
                                  <p><b>Abstract:</b> {{ article['abstract']}}...</p>
                                  <p><b>Submitted:</b> {{ article['submission']}}</p>
                              </li>
                              {% endfor %}
                              {% else %}

                              There are no articles to display :(

                              {% endif %}
                          </ul>
                          <ul class="tab content-pubmed-articles">
                              {% if pubmed_articles %}
                              {% for article in pubmed_articles|sort(reverse=true, attribute="score")%}
                              <li>
                                  <p><a href="https://pubmed.ncbi.nlm.nih.gov/{{article['docsum-pmid']}}"><b>Summary:</b> {{ article['summary'] }}</a></p>
                                  <p><b>Full Authors:</b> {{ article['full-authors'] }}</p>
                                  <p><b>Short Authors:</b> {{ article['short-authors'] }}</p>
                                  <p><b>Citation:</b> {{ article['citation'] }}</p>
                                  <p><b>Short Journal Citation:</b> {{ article['short-journal-citation'] }}</p>
                              </li>
                              {% endfor %}
                              {% else %}

                              There are no articles to display :(

                              {% endif %}
                          </ul>
                          <ul class="tab content-tweets">
                              {% if tweets %}
                              {% for tweet in tweets|sort(reverse=true, attribute="score")%}
                              <li>
                                  <p class="tweet">
                                      {{ tweet.tweet|urlize(40, target="_blank") }} <br/>
                                      by {{ tweet.author }}
                                  </p>
                                  <small class="timeposted">
                                      {{ tweet.timeposted }}
                                  </small>
                              </li>
                              {% endfor %}

                              {% else %}

                              There are no tweets to display :(

                              {% endif %}
                          </ul>
                          <ul class="tab content-commits">
                              {% if commits %}                              
                              {% for commit in commits|sort(reverse=true, attribute="score")%}
                              <li>
                                  <p class="commit">
                                      <a href="{{commit.url}}" target="_blank">
                                          {{ commit.hash.split(":")[-1][:7] }}:{{ commit.content}}
                                      </a>
                                      
                                  </p>
                                  <small class="timeposted">
                                      <a href="{{ commit['repository-url']}}" target="_blank">{{ commit.author }}/{{ commit.repository }}</a>
                                       on {{ commit.timeposted}}
                                  </small>
                              </li>
                              {% endfor %}
                              {% else %}
                              There are no commits to be displayed.
                              {%  endif %}
                          </ul>
                      </div>
                  </section>

                  <a href="https://projectredcap.org/"><img class="img-right" src="static/image/REDCap.png" /></a>
                  <p>
                    Make your sequence
                    data <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR</a>. Upload
                    your SARS-CoV-2 sequence (FASTA or FASTQ formats)
                    with simple metadata (JSONLD) to
                    the <a href="/about">public sequence
                    resource</a>. The upload will trigger a recompute
                    with all available sequences into a Pangenome
                    available for
                    <a href="/download">download</a>!
                  </p>
                  <p>
                    Your uploaded sequence will automatically be
                    processed and incorporated into the public
                    pangenome with metadata using worklows from the
                    High Performance Open Biology Lab
                    defined <a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>. All
                    data is published under
                    a <a href="https://creativecommons.org/licenses/by/4.0/">Creative
                    Commons license</a> You can take the published
                    (GFA/RDF/FASTA) data and store it in a triple
                    store for further processing.
                    Clinical data can
                    be stored securely
                    at <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>.
                  </p>
                  <a href="https://nanoporetech.com/"><img class="img-right" src="static/image/oxford-nanopore2.jpg" /></a>
                  <p>
                    Data can be uploaded from any sequencing platform
                    in FASTA format. We give special attention to
                    workflows for
                    the <a href="https://nanoporetech.com/">Oxford
                    Nanopore</a> - see
                    also <a href="https://pubmed.ncbi.nlm.nih.gov/?term=sars-cov-2+nanopore&sort=date">pubmed</a>
                    - because it offers an affordable platform that is
                    great for SARS-CoV-2 sequencing and
                    identification. In New Zealand the Oxford Nanopore
                    is used for all
                    <a href="https://www.esr.cri.nz/home/about-esr/media-releases/esr-performs-first-new-zealand-genome-sequencing-on-covid-19-sample/">tracing</a>.
                  </p>
                  <p>
                    Note that form fields contain
                    web <a href="https://en.wikipedia.org/wiki/Web_Ontology_Language">ontology
                    URI's</a>
                    for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a>
                    and machine readable metadata. For examples of
                    use, see the <a href="/blog">docs</a>.
                  </p>
                </div>
              </section>


      {% include 'footer.html' %}


      <script type="text/javascript">
        let scriptRoot = {{ request.script_root|tojson|safe }}; // examples

        drawMap()

      </script>

   </body>
</html>