Difference between revisions of "Team:Utrecht/"

 
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<div>
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<ul class="top-menu-links">
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<li data-key="home" class="active" data-url="home">Home</li>
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<li data-key="exp">Experimental</li>
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<li data-key="hp">Human practices</li>
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<li data-key="team">Team & Sponsors</li>
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</ul>
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<div class="quote"></div>
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<br />
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<div class="sections" data-key="exp">
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<div class="section" data-url="secretion">
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<div class="thumb"></div>
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<div class="text">Cas9 & Cpf1 secretion<br/>and activity</div>
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<div class="desc">Comparison of endonuclease activity for Cas9 and Cpf1 that has been produced in, and excreted by, HEK293 cells.</div>
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</div>
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<div class="section" data-url="mesa-replication">
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<div class="thumb"><img height="100" src="https://static.igem.org/mediawiki/2017/b/bc/MESA.png"></div>
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<div class="text">MESA two-component system replication</div>
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<div class="desc">Details on the MESA two-component system, explanation of its relation to our design and the results of its reproduction.</div>
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</div>
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<div class="section" data-url="outcasst">
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<div class="thumb"></div>
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<div class="text">OUTCASST system production</div>
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<div class="desc">Detailed explanation of the OUTCASST mechanism, experimental progress and technical prospects.</div>
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</div>
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<div class="section" data-url="modeling-and-mathematics">
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<div class="thumb"><img height="100" src="https://static.igem.org/mediawiki/2017/6/6b/Modelling.png"></div>
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<div class="text">Modeling and<br />mathematics</div>
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<div class="desc">Ordinary differential equations, cellular automaton and an object based model for optimal linker-length estimation.</div>
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</div>
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<div class="section" data-url="interlab-study">
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<div class="thumb"><img height="100" src="https://static.igem.org/mediawiki/2017/6/63/Interlab1.png"></div>
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<div class="text">Interlab study participation</div>
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<div class="desc">Results and details of our measurements for the iGEM 2017 Interlab Study.</div>
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</div>
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</div>
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<div class="sections" data-key="hp">
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<div class="section" data-url="stakeholders">
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<div class="thumb"></div>
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<div class="text">Stakeholders & opinions</div>
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<div class="desc">Interviews and dialogues with stakeholders, potential users, third parties and experts relating to pathogen detection or DNA-based diagnostics.</div>
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</div>
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<div class="section" data-url="safety">
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<div class="thumb"><img height="100" src="https://static.igem.org/mediawiki/2017/8/8d/Igemutrecht_safety.png"></div>
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<div class="text">Risks & safety-issues</div>
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<div class="desc">Implications and design considerations relating to safety in the usage and implementation of OUTCASST as a diagnostics tool.</div>
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</div>
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<div class="section" data-url="product-design">
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<div class="thumb"></div>
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<div class="text">Design & integration</div>
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<div class="desc">OUTCASST toolkit and product design with factors such as bio-safety and user-friendliness taken into account.</div>
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</div>
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</div>
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<div class="sections" data-key="team">
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<div class="section" data-url="team">
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<div class="thumb"><img height="100" src="https://static.igem.org/mediawiki/2017/5/5e/Team_comp.png"></div>
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<div class="text">Meet our team</div>
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<div class="desc">About us, our interests and roles in the team and our supervisors.</div>
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</div>
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<div class="section" data-url="sponsors">
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<div class="thumb"></div>
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<div class="text">Sponsors</div>
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<div class="desc">A listing of our sponsors, how they assisted us and our gratitude for their assistance.</div>
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</div>
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<div class="section" data-url="achievements">
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<div class="thumb"><img height="100" src="https://static.igem.org/mediawiki/2017/6/64/Achievements.png"></div>
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<div class="text">Achievements</div>
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<div class="desc">A short description of all that we have achieved during our participation in the iGEM.</div>
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</div>
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</div>
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</div>
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</div>
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<div class="menu-container">
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<div class="item active" data-key="1">
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<div class="marker"><div></div></div>
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<div class="text">Intro</div>
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<div class="item" data-key="2">
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<div class="marker"><div></div></div>
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<div class="text">The problem</div>
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</div>
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<div class="item" data-key="3">
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<div class="marker"><div></div></div>
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<div class="text">The system</div>
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<div class="page-container">
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<div class="page-content">
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<div class="page-heading">The OUTCASST two-component system</div>
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This year, Utrecht University participates in the iGEM for the first time. We aim to create a cheap DNA detection kit for disease diagnosis that is easy to use and does not rely on complicated sequencing technologies.
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<br />
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<br />
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<h2 class="subhead" id="subhead-2">The problem</h2>
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Disease diagnosis is of great importance for healthcare. In developing countries, diagnoses often have to be made based on limited information, even though accurate disease determination based on pathogen specific DNA sequences is possible through sequencing technologies. These technologies, however, require specialised equipment and expertise that simply is not available everywhere. The OUTCASST two-component system and detection kit hopes to alleviate this problem.
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<img id="figure-4" style="position: absolute; top: 0; left: 125px; display: none;" src="https://static.igem.org/mediawiki/2017/e/ec/Tutorial_4.png">
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<div class="container" style="position: absolute; top: 50px; left: 0; width: 75px;">
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<span id="link-1" class="tutorial_button selected pulsing" style="font-size: 17px; width: 75px; height: 75px; line-height: 75px;">Start</span>
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<span id="link-2" class="tutorial_button">2</span>
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<span id="link-3" class="tutorial_button">3</span>
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<span id="link-4" class="tutorial_button">4</span>
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</center>
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<h2 class="subhead" id="subhead-3">The system</h2>
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The OUTCASST two-component system consists of two proteins, expressed to the membrane of a dryable cell. One of the proteins is a Cas9-fusion and the other contains Cpf1. Both proteins can be given a guide RNA that makes it bind to a specific, user-chosen, complementary sequence. When both proteins bind a DNA fragment from a sample, they co-localize, so that a transcription factor is released intracellularly which then induces an intracellular reporter mechanism such as a dye or fluorescent signal.
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<div id="popover-1">
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Binding of components with search-specific gRNA sequences.
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DNA sample fragment binds to one of the components.
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Fragment binding with both components induces co-localization.
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<br>
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<a href="#" class="btn blue" id="goto-4" style="margin: 0; padding: 10px 25px; font-size: 18px;">Next</a>
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Protease cleaves, transcription factor is released from complex.
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We interviewed a panel of world-renowned experts. By listening carefully, our project's direction was shaped and refined.
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<br>
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      </div>
+
    </figure>
+
<figure class="js-item column col-span shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(0px, 389px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
+
      <div class="aspect aspect--32x9">
+
        <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/c/cd/Patrick_en_Pieter-Jaap.jpg"></div>
+
      </div>
+
    </figure>
+
<figure class="js-item column shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(0px, 129px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
+
      <div class="aspect aspect--9x80">
+
        <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/5/59/Hugo_Snippert_%282%29.jpg"></div>
+
      </div>
+
    </figure>
+
<figure class="js-item column shuffle-item shuffle-item--visible" style="position: absolute; top: 0px; left: 0px; visibility: visible; will-change: transform; opacity: 1; transform: translate(675px, 260px) scale(1); transition-duration: 250ms; transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1); transition-property: transform, opacity;">
+
      <div class="aspect aspect--9x80">
+
        <div class="aspect__inner"><img src="https://static.igem.org/mediawiki/2017/d/d0/Titia_Sijen.JPG"></div>
+
      </div>
+
    </figure>
+
    <div class="column my-sizer-element"></div>
+
  </div>
+
</div>
+
 
+
<section class="timeline" style="width: 1000px; margin-left: -100px;">
+
  <div class="timeline-container" style="width: 100%;">
+
    <div class="timeline-item">
+
 
+
      <div class="timeline-img"></div>
+
 
+
      <div class="timeline-content timeline-card js--fadeInLeft">
+
        <div class="timeline-img-header">
+
          <h2>Westerdijk</h2>
+
        </div>
+
        <div class="date">10 OCT 2017</div>
+
        <p>The first person we talked to came from the Westerdijk Fungal Biodiversity Institute in Utrecht. Here, they perform mycological research, wherein they focus on the determination and classification of fungi&hellip;</p>
+
        <a class="bnt-more" href="javascript:void(0)">More</a>
+
      </div>
+
 
+
    </div> 
+
    <div class="timeline-item">
+
 
+
      <div class="timeline-img"></div>
+
 
+
      <div class="timeline-content timeline-card js--fadeInRight">
+
        <div class="timeline-img-header">
+
          <h2>UMCU</h2>
+
        </div>
+
        <div class="date">10 OCT 2017</div>
+
        <p>We used this information and went to two DNA genome diagnostic labs, one in Utrecht and one in Amsterdam. At the University Medical Center of Utrecht we talked about the non-invasive prenatal testing and the use of our system to test for genetic conditions&hellip;</p>
+
        <a class="bnt-more" href="javascript:void(0)">More</a>
+
      </div>
+
 
+
    </div>   
+
 
+
  </div>
+
</section>
+
</script>
+
 
+
<style type="text/css">
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.shuffle-container .aspect:hover { opacity: 1; }
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.timeline .timeline-item::after {
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.timeline .timeline-content {
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.timeline .timeline-img {
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.timeline-card a {
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.timeline-item .timeline-img-header {
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  background-size: cover;
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}
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+
.timeline-img-header {
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  color: #FFFFFF;
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  position: absolute;
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  bottom: 5px;
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  left: 20px;
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}
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blockquote {
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  margin-top: 30px;
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  color: #757575;
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  border-left-color: #3F51B5;
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}
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.date {
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  background: #FF4081;
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  display: inline-block;
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  color: #FFFFFF;
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  padding: 10px;
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  position: absolute;
+
  top: 0;
+
  right: 0;
+
}
+
 
+
@media screen and (max-width: 768px) {
+
  .timeline::before {
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    left: 50px;
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  }
+
  .timeline .timeline-img {
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    left: 50px;
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  }
+
  .timeline .timeline-content {
+
    max-width: 100%;
+
    width: auto;
+
    margin-left: 70px;
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  }
+
  .timeline .timeline-item:nth-child(even) .timeline-content {
+
    float: none;
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  }
+
  .timeline .timeline-item:nth-child(odd) .timeline-content::after {
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    content: '';
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    position: absolute;
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    border-style: solid;
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    height: 0;
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    top: 30px;
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    border-width: 10px 15px 10px 0;
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}
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</style>
+
 
+
<script id="page-safety" type="text/template">
+
<div class="page-heading">Safety</div>
+
well important init
+
</script>
+
 
+
<script id="page-product-design" type="text/template">
+
<div class="page-heading">Product design</div>
+
1
+
</script>
+
 
+
<script id="page-team" type="text/template">
+
<div class="page-heading">Team</div>
+
1
+
</script>
+
 
+
<script id="page-sponsors" type="text/template">
+
<div class="page-heading">Sponsors</div>
+
1
+
</script>
+
 
+
<script id="page-achievements" type="text/template">
+
<div class="page-heading">Achievements</div>
+
1
+
</script>
+
+
<style type="text/css">
+
@import url(https://fonts.googleapis.com/css?family=Open+Sans);
+
 
+
/* set global font to Open Sans */
+
body {
+
  font-family: 'Open Sans', 'sans-serif';
+
  overflow: scroll;
+
}
+
 
+
.btn {
+
  border-radius: 5px;
+
  padding: 15px 25px;
+
  font-size: 22px;
+
  text-decoration: none;
+
  margin: 20px;
+
  color: #fff;
+
  position: relative;
+
  display: inline-block;
+
}
+
 
+
.btn:active {
+
  transform: translate(0px, 5px);
+
  -webkit-transform: translate(0px, 5px);
+
  box-shadow: 0px 1px 0px 0px;
+
}
+
 
+
.blue {
+
  background-color: #55acee;
+
  box-shadow: 0px 5px 0px 0px #3C93D5;
+
}
+
 
+
.blue:hover {
+
  background-color: #6FC6FF;
+
}
+
</style>
+
+
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
+
<script src='https://cdn3.devexpress.com/jslib/17.1.3/js/dx.all.js'></script>
+
<script type="text/javascript">
+
$.noConflict();
+
 
+
function getPos(el)
+
{
+
for (var lx=0, ly=0;
+
el != null;
+
lx += el.offsetLeft, ly += el.offsetTop, el = el.offsetParent);
+
return {x: lx,y: ly};
+
}
+
+
jQuery( window ).scroll(function() {
+
  var sel_subhead = 1;
+
+
jQuery(".subhead").each(function(k, v)
+
{
+
var key = v.id.split("-")[1];
+
+
var pos = getPos(v);
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+
if(jQuery(window).scrollTop() + 200 >= pos.y)
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{
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sel_subhead = key;
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}
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else if(Math.ceil(jQuery(window).scrollTop() + jQuery(window).height()) >= jQuery(document).height())
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{
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if(key == 3)
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{
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sel_subhead = key;
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}
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});
+
+
jQuery(".menu-container .item").each(function(k, v)
+
{
+
var key = v.getAttribute("data-key");
+
+
if(key == sel_subhead)
+
jQuery(v).addClass("active");
+
else
+
jQuery(v).removeClass("active");
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});
+
});
+
+
jQuery(function(){
+
for(var i = 1; i <= 4; i++)
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{
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var position = "left";
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var showEvent = "";
+
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if(i == 2 || i == 4)
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{
+
position = "right";
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showEvent = "";
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}
+
+
var title;
+
+
if(i == 1)
+
title = "Guide RNA";
+
else if(i == 2)
+
title = "DNA binding";
+
else if(i == 3)
+
title = "Signal transduction";
+
else if(i == 4)
+
title = "Signal transduction";
+
+
jQuery("#popover-" + i).dxPopover({
+
target: "#link-" + i,
+
showEvent: showEvent,
+
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+
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+
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+
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+
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+
+
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+
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+
+
jQuery('body').on('click', 'a', function(event) {
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var id = event.target.id;
+
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if(id == "goto-2")
+
{
+
jQuery("#link-1").removeClass("selected");
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+
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+
jQuery("#figure-3").fadeOut("5");
+
jQuery("#figure-4").fadeIn("5");
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}
+
});
+
});
+
</script>
+
 
+
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/prototype/1.7.2.0/prototype.js"></script>
+
<script src="https://ajax.googleapis.com/ajax/libs/scriptaculous/1.9.0/scriptaculous.js"></script>
+
 
+
<script type="text/javascript">
+
var page_menus = {
+
"home" : {
+
1: "Intro",
+
2: "The problem",
+
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"secretion" : {
+
1: "Secretion",
+
2: "Hmmmm"
+
},
+
"mesa-replication" : {
+
1: "MESA replication",
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2: "Hmmmm"
+
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2: "Hmmmm"
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+
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+
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+
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+
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+
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+
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+
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+
1: "Achievements",
+
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+
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+
 
+
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+
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+
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+
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+
+
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+
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+
line.style.width = width + "px";
+
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+
 
+
function change_page(page)
+
{
+
if(typeof page_menus[page] !== "undefined")
+
{
+
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+
+
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+
+
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+
+
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+
{
+
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+
+
$H(menu).each(function(pair)
+
{
+
new_html = new_html + "<div class='item' data-key='" + pair.key + "'><div class='marker'><div></div></div><div class='text'>" + pair.value + "</div></div>";
+
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+
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+
+
menu_container.update(new_html);
+
}
+
+
var page_container = $$(".page-content")[0];
+
var page_content = $("page-" + page);
+
+
page_container.update(page_content.innerHTML);
+
+
$$(".top-menu")[0].removeClassName("active");
+
$$(".menu-container")[0].removeClassName("active");
+
}
+
 
+
document.observe("dom:loaded", function()
+
{
+
move_underline($$(".top-menu-links li")[0]);
+
+
$$(".top-menu")[0].observe("mouseover", function()
+
{
+
this.addClassName("active");
+
$$(".menu-container")[0].addClassName("active");
+
});
+
+
$$(".top-menu")[0].observe("mouseout", function()
+
{
+
this.removeClassName("active");
+
$$(".menu-container")[0].removeClassName("active");
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});
+
 
+
$$(".top-menu")[0].on("click", ".section", function(event, element)
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{
+
var title = element.select(".text")[0].innerHTML;
+
var page = element.getAttribute("data-url");
+
+
//history.pushState({}, title, page);
+
+
change_page(page);
+
});
+
+
$$(".top-menu")[0].on("mouseover", ".section", function(event, element)
+
{
+
element.addClassName("active");
+
});
+
+
$$(".top-menu")[0].on("mouseout", ".section", function(event, element)
+
{
+
element.removeClassName("active");
+
});
+
+
$$(".top-menu-links")[0].on("click", "li", function(event, element)
+
{
+
var page = element.getAttribute("data-url");
+
+
if(page != "")
+
{
+
var title = page;
+
+
change_page(page);
+
+
if(page == "home")
+
page = "/";
+
+
//history.pushState({}, title, page);
+
}
+
});
+
+
$$(".top-menu-links")[0].on("mouseover", "li", function(event, element)
+
{
+
move_underline(element);
+
+
$$(".top-menu")[0].setAttribute("data-key", element.getAttribute("data-key"));
+
});
+
+
$$(".menu-container")[0].on("mouseover", ".item", function(event, element)
+
{
+
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+
});
+
+
$$(".menu-container")[0].on("mouseout", ".item", function(event, element)
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{
+
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+
});
+
+
Event.observe(window, "scroll", function()
+
{
+
var pos_y = 125 - window.scrollY;
+
+
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+
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+
+
//$$(".menu-container")[0].style.top = pos_y + "px";
+
});
+
});
+
</script>
+
 
+
<style class="cp-pen-styles">/* quick grid */
+
.shuffle-container {
+
  width: 93%;
+
  margin: auto;
+
}
+
 
+
/* Bootstrap-style columns */
+
.shuffle-container .column {
+
  position: relative;
+
  float: left;
+
  min-height: 1px;
+
  width: 25%;
+
  padding-left: 4px;
+
  padding-right: 4px;
+
 
+
  /* Space between tiles */
+
  margin-top: 8px;
+
}
+
 
+
.shuffle-container .col-span {
+
  width: 50%;
+
}
+
 
+
.shuffle-container .my-sizer-element {
+
  width: 8.33333%;
+
}
+
 
+
/* default styles so shuffle doesn't have to set them (it will if they're missing) */
+
.shuffle-container .my-shuffle {
+
  position: relative;
+
  overflow: hidden;
+
}
+
 
+
/* Ensure images take up the same space when they load */
+
/* https://vestride.github.io/Shuffle/images */
+
.shuffle-container .aspect {
+
  position: relative;
+
  width: 100%;
+
  height: 0;
+
  padding-bottom: 100%;
+
  overflow: hidden;
+
  opacity: 0.5;
+
}
+
 
+
.shuffle-container .aspect__inner {
+
  position: absolute;
+
  top: 0;
+
  right: 0;
+
  bottom: 0;
+
  left: 0;
+
}
+
 
+
.shuffle-container .aspect--16x9 {
+
  padding-bottom: 56.25%;
+
}
+
 
+
.shuffle-container .aspect--9x80 {
+
  padding-bottom: calc(112.5% + 8px);
+
}
+
 
+
.shuffle-container .aspect--32x9 {
+
  padding-bottom: calc(28.125% - 3px);
+
}
+
 
+
.shuffle-container img {
+
  display: block;
+
  width: 100%;
+
 
+
  max-width: none;
+
  height: 100%;
+
  -o-object-fit: cover;
+
    object-fit: cover;
+
}
+
 
+
/* Small reset */
+
.shuffle-container *,
+
.shuffle-container ::before,
+
.shuffle-container ::after {
+
  box-sizing: border-box;
+
}
+
 
+
.shuffle-container figure {
+
  margin: 0;
+
  padding: 0;
+
}</style>
+
 
+
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/Shuffle/5.0.2/shuffle.min.js"></script>
+
<script type="text/javascript">
+
/*var Shuffle = window.Shuffle;
+
 
+
var myShuffle = new Shuffle(document.querySelector('.my-shuffle'), {
+
  itemSelector: '.js-item',
+
  sizer: '.my-sizer-element',
+
  buffer: 1,
+
});*/
+
</script>
+
 
+
</body>
+
</html>
+

Latest revision as of 16:59, 27 October 2017

<!DOCTYPE html>

Cas9 & Cpf1 secretion
and activity
Comparison of endonuclease activity for Cas9 and Cpf1 that has been produced in, and excreted by, HEK293 cells.
MESA two-component system replication
Details on the MESA two-component system, explanation of its relation to our design and the results of its reproduction.
OUTCASST system production
Detailed explanation of the OUTCASST mechanism, experimental progress and technical prospects.
Modeling and
mathematics
Ordinary differential equations, cellular automaton and an object based model for optimal linker-length estimation.
InterLab study participation
Results and details of our measurements for the iGEM 2017 InterLab Study.
Stakeholders & opinions
Interviews and dialogues with stakeholders, potential users, third parties and experts relating to pathogen detection or DNA-based diagnostics.
Risks & safety-issues
Implications and design considerations relating to safety in the usage and implementation of OUTCASST as a diagnostics tool.
Design & integration
OUTCASST toolkit and product design with factors such as bio-safety and user-friendliness taken into account.
Outreach
Videos we made for the dutch public, together with 'de Kennis van Nu'.
Meet our team
About us, our interests and roles in the team and our supervisors.
Sponsors
A listing of our sponsors, how they assisted us and our gratitude for their assistance.
Collaborations
Read about our exchanges with other iGEM teams and government agencies.
Achievements
A short description of all that we have achieved during our participation in the iGEM.
Attributions
A thank-you for everyone that assited us, both in and outside the lab.