Difference between revisions of "Team:Munich"

Line 1: Line 1:
 +
 
<html>
 
<html>
 
<head>
 
<head>
−
     <style>
+
 
−
      
+
     <meta name="viewport" content="width=device-width" />
 +
     <script src = "https://2017.igem.org/Template:Munich/Javascript?action=raw&ctype=text/javascript"></script>
 +
    <link rel="stylesheet" type="text/css" href="https://2017.igem.org/Template:Munich/CSS?action=raw&ctype=text/css">
 +
 
 +
 
 +
 
 +
<style type="text/css">
 
     #home_logo, #sideMenu { display:none; }
 
     #home_logo, #sideMenu { display:none; }
 
     #sideMenu, #top_title, .patrollink  {display:none;}
 
     #sideMenu, #top_title, .patrollink  {display:none;}
Line 9: Line 16:
 
     #bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 { margin-bottom: 0px; }
 
     #bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 { margin-bottom: 0px; }
  
−
     </style>
+
     .navigation-bar{
 +
  background-color: white !important;
 +
}
  
 +
  #HQ_page p{
 +
  color: rgb(147,149,152);
 +
  font-family: Helvetica, Arial, sans-serif;
 +
  font-size: initial; 
 +
  }
 +
 +
.ui.secondary.menu.navigation-bar > div.ui.item{
 +
  padding: 0;
 +
}
 +
 +
 +
.cascaid{
 +
  width: 150px;
 +
  height: auto;
 +
}
 +
 +
section{
 +
  width: 66%;
 +
  margin: auto;
 +
}
 +
 +
#introduction{
 +
  margin-bottom: 10vh;
 +
}
 +
 +
.mybutton{
 +
  border-radius: 5px;
 +
  color: white;
 +
  border-color: transparent;
 +
}
 +
 +
h1.myHeader1{
 +
  font-size: 4vw;
 +
  text-align: center;
 +
  margin-top: 10vh;
 +
}
 +
 +
#introImgContainer{
 +
  text-align: center;
 +
}
 +
 +
img.introImg{
 +
  width: 70%;
 +
  height: auto;
 +
  margin-top: 10vh; /*Changed in comparision to the main structure, since there is no title here, but instead just an img*/
 +
}
 +
 +
.text{
 +
  color: rgb(147,149,152) !important;
 +
}
 +
.myImg{
 +
  width: 100%;
 +
  height: auto;
 +
}
 +
 +
p.myParagraph{
 +
  text-align: justify;
 +
 +
 +
}
 +
 +
.topicContainer > .figureContainer{
 +
  width: 66%;
 +
  margin: auto;
 +
  margin-top: 5vh;
 +
  margin-bottom: 5vh;
 +
}
 +
 +
 +
.float-right.figureContainer{
 +
  width: 33%;
 +
  border: 2px solid black;
 +
  margin: 1rem;
 +
  padding: 1rem;
 +
}
 +
 +
p.introP{
 +
  margin-top: 5vh;
 +
  margin-bottom: 5vh;
 +
 +
}
 +
 +
.float-right{
 +
  float: right;
 +
}
 +
 +
/* Lightbox CSS*/
 +
.lightbox{
 +
  display: none;
 +
  width: 100%;
 +
  height: 100%;
 +
  background-color: rgba(0,0,0,.7);
 +
  position: fixed;
 +
  top: 0;
 +
  left: 0;
 +
  z-index: 102;
 +
  padding-top: 30px;
 +
  box-sizing: border-box;
 +
}
 +
 +
.lightboxContainer{
 +
  position: relative;
 +
  top: 50%;
 +
  transform: translateY(-50%);
 +
 +
 +
}
 +
 +
.lightbox img{
 +
  display: block;
 +
  margin: auto;
 +
  max-width: 33vw;
 +
}
 +
 +
.lightbox .caption{
 +
  margin: 15px auto;
 +
  width: 50%;
 +
  text-align: center;
 +
  font-size: 1em;
 +
  line-height: 1.5;
 +
  font-weight: 700;
 +
  color: #eee;
 +
}
 
      
 
      
−
<link rel="stylesheet" type="text/css" href="https://2017.igem.org/Template:Munich/CSS?action=raw&ctype=text/css" />
+
.tooltip-line{
 +
      stroke: rgb(147,149,152);
 +
    }
  
−
<script type="text/javascript" src="https://2017.igem.org/Template:Munich/Javascript?action=raw&ctype=text/javascript"></script>
+
  .myvisible{
 +
    -webkit-animation: myvisible 1s linear;
 +
    -webkit-animation-fill-mode: forwards;
 +
  }
  
−
     <style type="text/css">
+
  @keyframes myvisible{
−
       
+
     0%{
−
        .ui.menu .just.item{
+
      opacity: 0;
−
                color: rgb(255, 255, 255);
+
    }
−
                background: rgba(255, 255, 255, 1.00);
+
    100%{
−
                padding: 0;
+
      opacity: 1;
−
        }
+
    }
 +
  }
 +
 
 +
  .colorNegative{
 +
    -webkit-animation: colorNegative 2s linear;
 +
    -webkit-animation-fill-mode: forwards;
 +
  }
 +
 
 +
  @keyframes colorNegative{
 +
    0%{
 +
      fill: white;
 +
    }
 +
 
 +
    100%{
 +
      fill: rgb(0,174,239);
 +
    }
 +
  } /* Because CSS is such a wonderful language, it is imperative to have the colorNegative definitions AFTER the visible one; otherwise the visible overwrites the colorNegative and the circles expand at the end, but don't change color.*/
 +
 
 +
 
 +
  .invisible{
 +
    opacity: 0;
 +
  }
 +
 
 +
  .appear{
 +
    -webkit-animation: appear 1s linear;
 +
  }
 +
 
 +
  @keyframes appear {
 +
    0%{
 +
      opacity: 0;
 +
    }
 +
 
 +
    100%{
 +
      opacity: 1;
 +
    }
 +
  }
 +
  .white{
 +
    -webkit-animation: white 1s linear;
 +
    -webkit-animation-fill-mode: forwards;
 +
  }
 +
 
 +
  @keyframes white{
 +
    0%{
 +
      fill: rgb(255,149,152);
 +
    }
 +
    100%{
 +
      fill: white;
 +
    }
 +
  }
 +
 
 +
.colorPositive{
 +
    -webkit-animation: colorPositive 2s linear;
 +
    -webkit-animation-fill-mode: forwards;
 +
  }
 +
 
 +
  @keyframes colorPositive{
 +
    0%{
 +
      fill:white;
 +
    }
 +
 
 +
    100%{
 +
      fill: rgb(100,255,0);
 +
    }
 +
  }
 +
 
 +
.explanation{
 +
    /*border-width: 30px;
 +
      border-radius: 10%; For when there is svg canvas in the divs */
 +
      border-radius: 30px;
 +
      border: 5px solid rgb(147,149,152);
 +
      padding: 10px;
 +
      margin-left: -1rem;   
 +
      color: rgb(147,149,152);
 +
      position: absolute;
 +
      top: 0;
 +
      left:0;
 +
      background-color: white;
 +
      max-width: 40vw;
 +
      display: flex;     
 +
  }
 +
 
 +
.explanation-text{
 +
  max-width: 25vw;
 +
}
 +
 
 +
  .pretty-picture{
 +
    width: auto;
 +
    height: 20vh;
 +
  }
 +
 
 +
  button{
 +
      font-family: Helvetica, Arial, sans-serif !important;
 +
      position: absolute;
 +
      right: 16.67%;
 +
      z-index: 41;
 +
  }
 +
 
 +
 
 +
  line{
 +
    stroke: rgb(147,149,152);
 +
  }
 +
 
 +
  .skip-animation{
 +
    background-color: rgb(0,174,239) !important;
 +
  }
 +
 
 +
@media screen and (max-width: 992px){
 +
  h1.myHeader1{
 +
    font-size: 40px;
 +
   
 +
  }
 +
 
 +
  .float-right.figureContainer{
 +
    width: 100%;
 +
    padding: 1rem;
 +
    margin: 0;
 +
  }
 +
 
 +
 
 +
  .topicContainer> .figureContainer{
 +
    width: 100%;
 +
    padding: 1rem;
 +
    margin: 0;
 +
  }
 +
 
 +
  .float-right{
 +
    float: none;
 +
  }
 +
 
 +
  .lightbox img{
 +
    max-width: 90vw;
 +
  }
 +
 
 +
  .lightbox .caption{
 +
    width: 90vw;
 +
  }
 +
 
 +
  .explanation-text{
 +
    display: none;
 +
  }
 +
  .pretty-picture{
 +
    width: auto;
 +
    height: 7vh;
 +
  }
 +
  .explanation{
 +
    border-width: 2px;
 +
    border-radius: 3px;
 +
  }
 +
 
 +
  .mybutton{
 +
   
 +
  }
 +
 
 +
}</style>
  
−
        .ui.tiny.image, .ui.tiny.images .image, .ui.tiny.images img, .ui.tiny.images svg{
 
−
            height: 55px;
 
−
            width: auto;
 
−
            font-size: .95714286rem;
 
−
            padding: 0;
 
−
        }
 
−
    </style>
 
 
</head>
 
</head>
−
<body>
+
<body onresize="renderDevice();calculateEndsteps();skipAnimation()">
 +
<div class=" ui fixed secondary menu grid">
 +
    <div class="ui computer only fixed seven item secondary menu row navigation-bar">
 +
      <div class="ui just item">
 +
            <img class="ui cascaid image" src="https://static.igem.org/mediawiki/2017/thumb/a/af/T--Munich--Logo_Final.svg/739px-T--Munich--Logo_Final.svg.png">
 +
        </div>
 +
        <div class="ui dropdown item" tabindex="0">
 +
            <div class="text">Project</div>
 +
            <div class="ui menu" tabindex="-1">
 +
                <a class="active item">Description</a>
 +
                <a class="disabled item">Interlab</a>
 +
            </div>
 +
        </div>
 +
        <div class="ui disabled dropdown item" tabindex="0">
 +
            <div class="text">Design</div>
 +
            <div class="ui menu" tabindex="-1">
 +
                <a class="item">Overall</a>
 +
                <a class="item">Parts</a>
 +
                <a class="item">Hardware</a>
 +
                <a class="item">Software</a>
 +
                <a class="item">Modeling</a>
 +
            </div>
 +
        </div>
 +
        <div class="ui dropdown item" tabindex="0">
 +
            <div class="text">Lab</div>
 +
            <div class="ui menu" tabindex="-1">
 +
                <a class="item">Lab journal</a>
 +
                <a class="disabled item">Experiments</a>
 +
                <a class="disabled item">Results</a>
 +
                <a class="disabled item">Safety</a>
 +
            </div>
 +
        </div>
  
 +
        <div class="ui dropdown item" tabindex="0">
 +
            <div class="text">Team</div>
 +
            <div class="ui menu" tabindex="-1">
 +
                <a class="item" href="https://2017.igem.org/Team:Munich/Team">The Team</a>
 +
                <a class="disabled item">Attributions</a>
 +
                <a class="disabled item">Collaborations</a>
 +
            </div>
 +
        </div>
  
 +
        <div class="ui disabled dropdown item" tabindex="0">
 +
            <div class="text">Human Practices</div>
 +
            <div class="ui menu" tabindex="-1">
 +
                <a class="item">Awards</a>
 +
                <a class="item">Medals</a>
 +
            </div>
 +
        </div>
  
−
<div class='ui seven item secondary menu'>
+
        <div class="ui disabled dropdown item" tabindex="0">
−
    <div class='ui just item'>
+
            <div class="text">Awards</div>
−
        <img class='ui tiny cascaid image' src="https://static.igem.org/mediawiki/2017/a/af/T--Munich--Logo_Final.svg">
+
            <div class="ui menu" tabindex="-1">
−
    </div>
+
                <a class="item">Special prizes</a>
−
    <div class='ui dropdown item'>
+
                <a class="item">Medals</a>
−
        Project
+
            </div>
−
        <div class='ui menu'>
+
−
            <a class="active item">Description</a>
+
−
            <a class="disabled item">Interlab</a>
+
 
         </div>
 
         </div>
 
     </div>
 
     </div>
−
     <div class='ui disabled dropdown item'>
+
     <div class="ui mobile only fixed two item secondary menu row navigation-bar">
−
        <div class='text'>Design</div>
+
      <div class="ui just item">
−
        <div class='ui menu'>
+
             <img class="ui cascaid image" src="https://static.igem.org/mediawiki/2017/thumb/a/af/T--Munich--Logo_Final.svg/739px-T--Munich--Logo_Final.svg.png">
−
            <a class="item">Overall</a>
+
−
             <a class="item">Parts</a>
+
−
            <a class="item">Hardware</a>
+
−
            <a class="item">Software</a>
+
−
            <a class="item">Modeling</a>
+
 
         </div>
 
         </div>
−
    </div>
+
        <div class="ui dropdown item" tabindex="0">
−
    <div class='ui disabled dropdown item'>
+
          <div class="text">
−
        <div class='text'>Lab</div>
+
            Menu
−
        <div class='ui menu'>
+
          </div>
−
            <a class="item">Lab journal</a>
+
          <div class="ui menu" tabindex="-1">
−
            <a class="item">Experiments</a>
+
            <div class="ui item accordion">
−
            <a class="item">Results</a>
+
              <div class="title">Project</div>
−
            <a class="item">Safety</a>
+
              <div class="ui content bulleted list">
 +
                <div class="">Description</div>
 +
                <div class="">Interlab</div>
 +
              </div>
 +
             
 +
              <div class="title">Design</div>
 +
              <div class="ui content bulleted list">
 +
                <div class="">Overall</div>
 +
                <div class="">Parts</div>
 +
                <div class="">Hardware</div>
 +
                <div class="">Software</div>
 +
                <div class="">Modeling</div>
 +
              </div>
 +
             
 +
              <div class="title">Lab</div>
 +
              <div class="ui content bulleted list">
 +
                <div class="">Lab journal</div>
 +
                <div class="">Experiments</div>
 +
                <div class="">Safety</div>
 +
              </div>
 +
             
 +
              <div class="title">Team</div>
 +
              <div class="ui content bulleted list">
 +
                <div class="">Team Members</div>
 +
                <div class="">Attributions</div>
 +
                <div class="">Collaboration</div>
 +
              </div>
 +
             
 +
              <div class="title">Human Practices</div>
 +
              <div class="ui content bulleted list">
 +
                <div class="">Awards</div>
 +
                <div class="">Medals</div>
 +
              </div>
 +
             
 +
              <div class="title">Awards</div>
 +
              <div class="ui content bulleted list">
 +
                <div class="">Special prizes</div>
 +
                <div class="">Medals</div>
 +
              </div>
 +
             
 +
            </div>         
 +
          </div>
 
         </div>
 
         </div>
 +
       
 
     </div>
 
     </div>
 +
    <div class="ui tablet only fixed seven item secondary menu row navigation-bar">
 +
      <div class="ui just item">
 +
            <img class="ui cascaid image" src="https://static.igem.org/mediawiki/2017/thumb/a/af/T--Munich--Logo_Final.svg/739px-T--Munich--Logo_Final.svg.png">
 +
        </div>
 +
        <div class="ui dropdown item" tabindex="0">
 +
            Tablet
 +
            <div class="ui menu" tabindex="-1">
 +
                <a class="active item">Description</a>
 +
                <a class="disabled item">Interlab</a>
 +
            </div>
 +
        </div>
 +
        <div class="ui disabled dropdown item" tabindex="0">
 +
            <div class="text">Design</div>
 +
            <div class="ui menu" tabindex="-1">
 +
                <a class="item">Overall</a>
 +
                <a class="item">Parts</a>
 +
                <a class="item">Hardware</a>
 +
                <a class="item">Software</a>
 +
                <a class="item">Modeling</a>
 +
            </div>
 +
        </div>
 +
        <div class="ui dropdown item" tabindex="0">
 +
            <div class="text">Lab</div>
 +
            <div class="ui menu" tabindex="-1">
 +
                <a class="item">Lab journal</a>
 +
                <a class="disabled item">Experiments</a>
 +
                <a class="disabled item">Results</a>
 +
                <a class="disabled item">Safety</a>
 +
            </div>
 +
        </div>
  
−
    <div class='ui dropdown item'>
+
        <div class="ui dropdown item" tabindex="0">
−
        <div class="text">Team</div>
+
            <div class="text">Team</div>
−
        <div class='ui menu'>
+
            <div class="ui menu" tabindex="-1">
−
            <a class="item" href="https://2017.igem.org/Team:Munich/Team">The Team</a>
+
                <a class="item" href="https://2017.igem.org/Team:Munich/Team">The Team</a>
−
            <a class="disabled item">Attributions</a>
+
                <a class="disabled item">Attributions</a>
−
            <a class="disabled item">Collaborations</a>
+
                <a class="disabled item">Collaborations</a>
 +
            </div>
 
         </div>
 
         </div>
−
    </div>
 
  
−
    <div class='ui disabled dropdown item'>
+
        <div class="ui disabled dropdown item" tabindex="0">
−
        <div class='text'>Human Practices</div>
+
            <div class="text">Human Practices</div>
−
        <div class='ui menu'>
+
            <div class="ui menu" tabindex="-1">
−
            <a class="item">Awards</a>
+
                <a class="item">Awards</a>
−
            <a class="item">Medals</a>
+
                <a class="item">Medals</a>
 +
            </div>
 
         </div>
 
         </div>
−
    </div>
 
  
−
    <div class='ui disabled dropdown item'>
+
        <div class="ui disabled dropdown item" tabindex="0">
−
        <div class='text'>Awards</div>
+
            <div class="text">Awards</div>
−
        <div class='ui menu'>
+
            <div class="ui menu" tabindex="-1">
−
            <a class="item">Special prizes</a>
+
                <a class="item">Special prizes</a>
−
            <a class="item">Medals</a>
+
                <a class="item">Medals</a>
 +
            </div>
 
         </div>
 
         </div>
 
     </div>
 
     </div>
 +
  </div>
  
−
</div>
+
<section id="introduction">
 +
  <div id="introImgContainer">
 +
    <img class="myImg introImg" src="https://static.igem.org/mediawiki/2017/thumb/a/af/T--Munich--Logo_Final.svg/739px-T--Munich--Logo_Final.svg.png"/ alt="intro Picture">
 +
  </div>
 +
  <div id="introPContainer">
 +
    <p class="myParagraph introP">
 +
      CascAID stands for Cas13a Controlled Assay for Infectious Diseases. Our goal this year is to create a novel paper-based microfluidic device for the detection of specific RNA sequences.
 +
      Nowadays, there is a trend among medical practitioners to prescribe antibiotics when bacterial infections are suspected without a laboratory confirmation as a way for speeding up recovery. This has led to an increase in antibiotic-resistant bacteria that makes it difficult to treat infected patients. Nucleic acid-based detection methods could allow for faster diagnosis. Therefore, we seek to develop a method that allows to report the presence of a specific pathogen within hours. For this reason, we will use the CRISPR effector Cas13a, which is able to target specific single-stranded RNA. This system allows for the simple and fast design of new sequence targets, being an ideal tool for detecting fast mutating pathogens. In the long term, we see our device as an easy-to-use and fast diagnostic tool in developing countries as well as an instrument in developed countries for discerning between bacterial and viral infections, that could help reducing antibiotics prescription.
 +
    </p>
 +
  </div>
 +
</section>
 +
<div style="position: relative;"> <!-- Dont' be lazy and change this at some point... -->
 +
  <button onclick="skipAnimation()" class ="mybutton skip-animation" >
 +
      <b>Skip animation</b>
 +
  </button>
 +
  <div id="canvas-container" >
 +
    <svg id="svg-canvas" >
 +
 
 +
      <circle fill="rgb(147,149,152)" id="top-circle" class="circle" />
 +
     
 +
     
 +
   
 +
      <line class="line-vertical" id="top-line" y1="-3"/>
 +
      <line class="line-vertical" id="bottom-line1" y1="-1"/>
 +
      <line class="line-vertical" id="bottom-line2" y1="-1"/>
 +
      <line class="line-vertical" id="bottom-line3" y1="-1"/>    <!-- It is important to put the bottom lines before the rect so the latter covers any gaps appearing due to rounding erros -->
 +
 
 +
      <rect fill="rgb(0,174,239)" rx="10" ry="10" id="device-body" fill="rgb(147,149,152)"/> <!-- Maybe the corners are too rounded? -->
 +
 
 +
      <line class="line-horizontal" id="horizontal-line1"/>
 +
      <line class="line-horizontal" id="horizontal-line2"/>
 +
 
 +
      <line class="line-vertical2" id="bottom-line4" y1="-1"/>
 +
      <line class="line-vertical2" id="bottom-line5" y1="-1"/>
 +
 
 +
      <circle fill="rgb(147,149,152)" id="bottom-circle1" class="circlebottom" />
 +
      <circle fill="rgb(147,149,152)" id="bottom-circle2" class="circlebottom" />
 +
      <circle fill="rgb(147,149,152)" id="bottom-circle3" class="circlebottom" />
 +
 
 +
 +
      <line class="tooltip-line" id="tooltip-line2" />
 +
 
 +
 +
      <line class="tooltip-line" id="tooltip-line3" />
 +
 
 +
 +
      <line class="tooltip-line" id="tooltip-line4" />
 +
 
 +
 +
      <line class="tooltip-line" id="tooltip-line5" />
 +
 
 +
      <circle class="pulse" fill="rgb(255,149,152)" id="pulse" />
 +
      <circle class="sample" fill="rgb(255,149,152)" id="sample" />
 +
 
 +
      <circle class="invisible pulse" fill="white" id="pulse2" />
 +
      <circle class="invisible sample"  fill="white" id="sample2" />
 +
 
 +
      <circle class="invisible pulse"  fill="white" id="pulse3" />
 +
      <circle class="invisible sample"  fill="white" id="sample3" />
 +
 
 +
 +
      <line class="tooltip-line" id="tooltip-line1" />  <!-- The first tooltip and circle are put here so they are on top of the sample -->
 +
    </svg>
 +
  </div>
 +
 
 +
    <div class="explanation explanation-left invisible" id="tip1">
 +
    <div class="pretty-picture-container">
 +
      <img class="pretty-picture lightboxAble" src="https://static.igem.org/mediawiki/2017/thumb/6/6b/T--Munich--FrontPage001.jpeg/800px-T--Munich--FrontPage001.jpeg" alt="<b>Step 1:</b><br>
 +
      A sample, such as blood or saliva, is placed into the device.">
 +
    </div>
 +
    <p class="explanation-text">
 +
      <b>Step 1:</b><br>
 +
      A sample, such as blood or saliva, is placed into the device.
 +
    </p>
 +
  </div>
 +
 
 +
   
 +
  <div class="explanation explanation-left invisible" id="tip3">
 +
    <div class="pretty-picture-container">
 +
      <img class="pretty-picture lightboxAble" src="https://static.igem.org/mediawiki/2017/thumb/6/68/T--Munich--FrontPage003.jpeg/800px-T--Munich--FrontPage003.jpeg">
 +
    </div>
 +
    <p class="explanation-text">
 +
      <b>Step 3: </b><br>
 +
      Cas13a binds the target sequence and cuts it in smaller fragments. After this inital digestion, the enzyme changes into a RNAase-active conformation.
 +
    </p>
 +
  </div>
 +
 
 +
  <div class="explanation explanation-left invisible" id="tip5">
 +
    <div class="pretty-picture-container">
 +
      <img class="pretty-picture" src="https://static.igem.org/mediawiki/2017/thumb/f/f6/T--Munich--FrontPage005.jpeg/800px-T--Munich--FrontPage005.jpeg">
 +
    </div>
 +
    <p class="explanation-text">
 +
      <b>Step 5:</b><br>
 +
      An easy to interpret read-out tells whether a specific pathogen was present in the sample.
 +
    </p>
 +
  </div>
 +
 
 +
    <div class="explanation explanation-right invisible" id="tip2">
 +
      <div class="pretty-picture-container">
 +
        <img class="pretty-picture lightboxAble" src="https://static.igem.org/mediawiki/2017/thumb/0/00/T--Munich--FrontPage002.jpeg/800px-T--Munich--FrontPage002.jpeg">
 +
      </div>
 +
      <p class="explanation-text">
 +
        <b>Step 2:</b><br>
 +
        RNA is purified with the help of our reusable, 3D-printed microfluidic device.
 +
      </p>
 +
    </div>
 +
    <div class="explanation explanation-right invisible" id="tip4">
 +
      <div class="pretty-picture-container">
 +
        <img class="pretty-picture lightboxAble" src="https://static.igem.org/mediawiki/2017/thumb/f/f0/T--Munich--FrontPage004.jpeg/800px-T--Munich--FrontPage004.jpeg">
 +
      </div>
 +
      <p class="explanation-text">
 +
        <b>Step 4:</b><br>
 +
        While in this conformation, Cas13a degrades the read-out RNA, producing a visible signal.
 +
      </p>
 +
    </div>
 +
 
  
 
<div class="ui bottom fixed icon menu">
 
<div class="ui bottom fixed icon menu">
Line 105: Line 615:
 
   </a>
 
   </a>
 
</div>
 
</div>
 +
    <script>
  
 +
//This script configures the svg-image to have a proportional size relative to the window-size
 +
  var animationstep;
  
−
<div class='ui two column grid container'>
+
  var pulsestep;
  
−
        <div class="column">
+
  var shiftcanvas;
−
            <p style="font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; font-weight: 700; font-size: 30px;">Problem</p>
+
−
            <div class='hidden horizontal divider'></div>
+
−
            <p style="font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; font-size: 14px;">Although there are many diagnostic tests available that can detect even the smallest traces of a pathogen, they usually require expensive lab-equipment or skilled labor. Usually, places most prone to diseases are also the ones most lacking such equipment or personal, and thus, where tests are least accesible. Many different diseases can present similar symptoms. But because the treatment for each of them can vary greatly (e.g. bacterial vs viral infection), a quick and reliable diagnostic is important to start as soon as possible with the right treatment. On the other hand, wrongly recognising the cause of a disease not only leads to prescription of the wrong medicine, but also can contribute to the spread of resistances.</p>
+
−
            <div class='hidden horizontal divider'></div>
+
  
−
            <p style="font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; font-size: 14px;">New diagnostic tool must take these points into consideration and be designed with affordability, availability, simplicity and reliability in mind, and, where possible, be flexible enough to cover a wide array of diseases in order to present the user with a single powerful product.</p>
+
  var canvaswidth;
−
             
+
−
        </div>
+
−
        <div class="column">
+
−
            <p style="font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; font-weight: 700; font-size: 30px;">Solution</p>
+
−
            <div class='hidden horizontal divider'></div>
+
−
            <p style="font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; font-size: 14px;">We are developing a diagnostic tool that combines the power of high sensible methods with the affordability needed for a wide application field. Our project, named CascAID, utilizes a CRISPR/Cas effector protein to quickly and reliably test for different pathogens based on their RNA. By cleverly designing a short RNA sequence, it is possible to guide this protein to cleave RNA molecules. If the sample contained pathogen, then digested RNA will be found, where as a negative sample won't produce digestion fragments.</p>
+
−
            <div class='hidden horizontal divider'></div>
+
  
−
            <p style="font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; font-size: 14px;">
+
  var devicewidth;
−
            In additon, we are trying to make CascAID an affordable but single use product thus reducing the risk of cross-contamination without increasing the production cost.
+
−
            </p>
+
−
        </div>
+
−
</div>
+
  
 +
  var circleradius;
  
 +
  var cycircle;
 +
 +
  var linewidth;
 +
 +
  var linelength;
 +
 +
  var deviceheight;
 +
 +
  var linelengthHor;
 +
 +
  var tooltipradius;
 +
 +
  var tooltiplinelength;
 +
 +
  var heightexplanation;
 +
 +
  var svgheight;
 +
 +
  var baserightLinelength; //This variable is responsible for setting a baselength for the tooltip lines. Changing it changes all tooltip lines, but keeping their ratios.
 +
 +
  var firstrender = true; //Boolean to differentiate whether it is the first time the device is being rendered or resizing is taking place.
 +
 +
  renderDevice();
 +
 +
 +
 +
 +
  function renderDevice(){
 +
    var hola;
 +
    if(!firstrender){
 +
     
 +
      hola = $("#sample").attr("cy")/svgheight; 
 +
    }
 +
 +
 
 +
 +
    deviceheightbefore = deviceheight //deviceheightbefore is only there to save a value before the resizing, so the elements of the device can be positioned accordingly.
 +
 +
    canvaswidth = window.innerWidth*0.80;
 
      
 
      
  
 +
    shiftcanvas = canvaswidth*0.1; //Shift canvas is there so make it easy to horizontally move the whole construct of svg-canvas and explanation
 +
 +
    devicewidth = window.innerWidth*0.0534;    //Defining the width of the deviece-rectangle, around which the whole desing is based.
 +
 +
    circleradius = devicewidth*0.5;
 +
 +
    circleradiusbottom = circleradius * 0.7;
 +
 +
    linewidth = devicewidth*0.1;
 +
 +
    linelength = devicewidth*0.33;
 +
 +
    if(window.innerWidth <= 768){
 +
      deviceheight = window.innerHeight*0.6;
 +
      tooltiplinelength = canvaswidth;
 +
      baserightLinelength = linelength*4.5; 
 +
    } else {
 +
      deviceheight = window.innerHeight*0.9;
 +
      tooltiplinelength = canvaswidth*0.1;
 +
      baserightLinelength = linelength*2; 
 +
    }
 +
 +
    linelengthbottom = linelength*2.3;   
 +
 +
    linelengthHor = linelength*2.5;
 +
 +
    tooltipradius = circleradius*0.20;
 +
 +
   
 +
 +
    heightexplanation = parseInt($(".explanation").css("height"));
 +
 +
   
 +
 +
    svgheight = deviceheight+devicewidth*6;
 +
 +
    cycircle = svgheight*0.05;
 +
 +
    animationstep = Math.ceil(9000/deviceheight); //Time in ms that each step of the animation needs. Increasing makes the animation slower.
 +
 +
    pulsestep = Math.ceil(2563/circleradius); //Time of the step in the pulse animation. Has to be different to animationstep, because the pulse cycle should be the same regardless of deivce size.
 +
 +
  $("#svg-canvas").attr("height",svgheight); //This two lines are to make sure the footer stays relatively close to the end of the device.
 +
 +
 +
  $("#svg-canvas").attr("width",canvaswidth+'');  //The Width of the canvas is defined
 +
 +
 +
 +
  $(".circle").attr("r",circleradius);   
 +
  $(".circlebottom").attr("r",circleradiusbottom); //The radius of the circles are defined.
 +
  $("#top-circle").attr("cx",canvaswidth*0.1+'');
 +
  $("#top-circle").attr("cy",cycircle+'');            //The position of the top-circle is defined.
 +
 +
 +
 
 +
 
 +
  $("#sample").attr("cx",canvaswidth*0.1);
 +
  if(firstrender) $("#sample").attr("cy",cycircle);              //The sample circle is defined. 
 +
  $("#sample").attr("r",circleradius);
 +
 +
 
 +
 +
  $("#pulse").attr("r",Math.max(circleradius*0.04,1));
 +
    $("#pulse").attr("cx",canvaswidth*0.1);
 +
    if(firstrender) $("#pulse").attr("cy",cycircle);                //The inital size and position of the pulse circle are defined.
 +
firstrender = false;   
 +
 +
 
 +
 
 +
 
 +
 +
 
 +
  $("line").css("stroke-width",linewidth+''); //The width of the lines is defined.
 +
 
 +
  $(".line-vertical").attr("y2",linelength+1+''); //The length of the vertical lines is defined. +1 is needed due to roundig errors.
 +
 +
  $(".line-vertical2").attr("y2",linelengthbottom+''); //The length of the other bottom lines is defined
 +
 +
  $("#top-line").css("transform","translate("+canvaswidth*0.1+"px,"+(cycircle+circleradius)+"px)"); //The top line is correctly positioned.
 +
 +
 
 +
  $("#device-body").attr("width",devicewidth);
 +
  $("#device-body").attr("height",deviceheight);
 +
  $("#device-body").attr("x",canvaswidth*0.1-devicewidth*0.5+'');
 +
  $("#device-body").attr("y",cycircle+circleradius+linelength+'');          //The width and position of the device-rectangle are defined.
 +
 +
  $("#sample2").attr("r",parseInt(circleradius*0.15));
 +
  $("#sample2").attr("cx",canvaswidth*0.1);
 +
  $("#sample2").attr("cy",parseInt(cycircle+linelength+circleradius+0.65*deviceheight)+1);
 +
  $("#pulse2").attr("r",circleradius*0.04);
 +
  $("#pulse2").attr("cx",canvaswidth*0.1);
 +
  $("#pulse2").attr("cy",parseInt(cycircle+linelength+circleradius+0.65*deviceheight)+1);
 +
 
 +
  $("#sample3").attr("r",parseInt(circleradius*0.15));
 +
  $("#sample3").attr("cx",canvaswidth*0.1);
 +
  $("#sample3").attr("cy",parseInt(cycircle+linelength+circleradius+0.65*deviceheight)+1);
 +
  $("#pulse3").attr("r",circleradius*0.04);
 +
  $("#pulse3").attr("cx",canvaswidth*0.1);
 +
  $("#pulse3").attr("cy",parseInt(cycircle+linelength+circleradius+0.65*deviceheight)+1); //Defining the two other circles that will show later in the animation.
 +
 
 +
 +
 +
  $("#bottom-line1").css("transform","translate("+parseInt(canvaswidth*0.1-0.3*devicewidth)+"px,"+(cycircle+deviceheight+linelength+circleradius)+"px)");
 +
 +
  $("#bottom-line2").attr("y2",linelength+linelengthbottom); //The line of the seconds line is increased
 +
  $("#bottom-line2").css("transform","translate("+(canvaswidth*0.1)+"px,"+(cycircle+deviceheight+linelength+circleradius)+"px)");
 +
 +
  $("#bottom-line3").css("transform","translate("+parseInt(canvaswidth*0.1+0.3*devicewidth)+"px,"+(cycircle+deviceheight+linelength+circleradius)+"px)"); //The position of the three bottom lines is defined.
 +
 +
 
 +
  $(".line-horizontal").attr("x2",linelengthHor);
 +
  $("#horizontal-line1").css("transform","translate("+(parseInt(canvaswidth*0.1-0.3*devicewidth)-linelengthHor+0.5*linewidth)+"px,"+(cycircle+deviceheight+2*linelength+circleradius)+"px)");
 +
  $("#horizontal-line2").css("transform","translate("+(parseInt(canvaswidth*0.1+0.3*devicewidth)-0.5*linewidth)+"px,"+(cycircle+deviceheight+2*linelength+circleradius)+"px)"); //The two horizontal lines are defined and positioned.
 +
 +
  $("#bottom-line4").css("transform","translate("+(parseInt(canvaswidth*0.1-0.3*devicewidth)-linelengthHor+linewidth)+"px,"+(cycircle+deviceheight+2*linelength+circleradius)+"px)");
 +
  $("#bottom-line5").css("transform","translate("+(parseInt(canvaswidth*0.1+0.3*devicewidth)+linelengthHor-linewidth)+"px,"+(cycircle+deviceheight+2*linelength+circleradius)+"px)"); //The two other vertical lines positioned.
 +
 
 +
  $("#bottom-circle1").css("transform","translate("+(parseInt(canvaswidth*0.1-0.3*devicewidth)-linelengthHor+linewidth)+"px,"+(cycircle+deviceheight+2*linelength+linelengthbottom+circleradius+circleradiusbottom-1)+"px)");
 +
  $("#bottom-circle2").css("transform","translate("+canvaswidth*0.1+"px,"+(cycircle+deviceheight+2*linelength+linelengthbottom+circleradius+circleradiusbottom-1)+"px)");
 +
  $("#bottom-circle3").css("transform","translate("+(parseInt(canvaswidth*0.1+0.3*devicewidth)+linelengthHor-linewidth)+"px,"+(cycircle+deviceheight+2*linelength+linelengthbottom+circleradius+circleradiusbottom-1)+"px)"); //The three bottom circles are positioned.
 +
 +
 +
 +
 +
  if(window.innerWidth <= 768){
 +
    $(".tooltip-line").css("stroke-width",2); 
 +
  } else {
 +
    $(".tooltip-line").css("stroke-width",5);
 +
  }
 +
 
 +
   
 +
  $(".tooltip-line").attr("x2",tooltiplinelength);  //The width and length of the tooltip lines are defined.
 +
  $(".tooltip-line").attr("stroke-linecap","round");
 +
 
 +
 +
 
 +
 +
  $("#tooltip-line1").css("transform","translate("+(canvaswidth*0.1+circleradius-1)+"px,"+cycircle+"px)");
 +
  $("#tooltip-line1").attr("x2",0);
 +
 +
  $("#tooltip-line2").css("transform","translate("+(canvaswidth*0.1+circleradius-1)+"px,"+(cycircle+circleradius+linelength+0.225*deviceheight)+"px)");
 +
  $("#tooltip-line2").attr("x2",0);
 +
 +
  $("#tooltip-line3").css("transform","translate("+(canvaswidth*0.1+circleradius-1)+"px,"+(cycircle+circleradius+linelength+0.55 *deviceheight)+"px)");
 +
  $("#tooltip-line3").attr("x2",0); 
 +
 +
  $("#tooltip-line4").css("transform","translate("+(canvaswidth*0.1+circleradius-1)+"px,"+(cycircle+circleradius+linelength+0.85*deviceheight)+"px)");
 +
  $("#tooltip-line4").attr("x2",0);
 +
  $("#tooltip-line5").css("transform","translate("+(canvaswidth*0.1+circleradius+linelengthHor+circleradiusbottom-0.3*devicewidth)+"px,"+(cycircle+deviceheight+2*linelength+linelengthbottom+circleradius+circleradiusbottom)+"px)");
 +
  $("#tooltip-line5").attr("x2",0);      //Depending whether the line point right or left, either x1 or x2 is changed to match the other value so the inial length of the lines is 0, rendering them invisible. This is later changed through the extendLine() function.
 +
 +
//Here we configure the tip boxes with javascript, because CSS sucks.
 +
//Important: unless every explanation has the same height, this won't work;
 +
 +
  $("#tip1").css("left",(canvaswidth*0.1+circleradius-1)+baserightLinelength+shiftcanvas+11); // For whatever reason, +11 alings the line with the
 +
  $("#tip1").css("top",cycircle-heightexplanation*0.5);
 +
 +
  $("#tip2").css("left",(canvaswidth*0.1+circleradius-1)+baserightLinelength*5+shiftcanvas);
 +
  $("#tip2").css("top",(cycircle+circleradius+linelength+0.225*deviceheight)-heightexplanation*0.5);
 +
 +
  $("#tip3").css("left",(canvaswidth*0.1+circleradius-1)+baserightLinelength*2.5+shiftcanvas+11);
 +
  $("#tip3").css("top",(cycircle+circleradius+linelength+0.55 *deviceheight)-heightexplanation*0.5);
 +
 +
  $("#tip4").css("left",(canvaswidth*0.1+circleradius-1)+baserightLinelength*6+shiftcanvas);
 +
  $("#tip4").css("top",(cycircle+circleradius+linelength+0.85*deviceheight)-heightexplanation*0.5);
 +
 +
  $("#tip5").css("left",(canvaswidth*0.1+circleradius+linelengthHor+circleradiusbottom-0.3*devicewidth)+baserightLinelength*2+shiftcanvas);
 +
  $("#tip5").css("top",(cycircle+deviceheight+2*linelength+linelengthbottom+circleradius+circleradiusbottom)-heightexplanation*0.5);
 +
  $(".button-container").css("left",$(".header-container").css("margin-left"));//Change this so it is calculated faster.
 +
  $(".button-container").css("top",cycircle-0.5*heightexplanation); //I literally don't know where to put the button...
 +
 +
  $("#svg-canvas").css("transform","translate("+shiftcanvas+"px,"+0);
 +
 +
  }
 +
 +
 +
 +
var animatinoCounter = 0;  //This counter saves the number of animation that have already been triggered. If an animation is not triggering, check if the counter-count is done propertly.
 +
var accu = 0;
 +
 +
$(window).on("scroll",checkPosition);    //Checks on every scroll whether a certain animation should be triggered or not.
 +
 
 +
var finalshrink = parseInt(circleradius*0.15);    //This variable is here so the shrink function doesn't have to evaluate parseIn(etc) every single time.
 +
 +
 +
var startMovement = false;                //This variable is the responsible for triggering the first moveCircleY. It's declared here so it is within scoope of all functions.
 +
 +
 +
 +
var endstep1; //This variable tells the first set of animations where they should end.
 +
var endstep2;              //This variable tells the second set of animations where they should end.
 +
var endstep3;
 +
 +
var endstep4;
 +
 +
var endstep5;
 +
 +
var endstep6;
 +
 +
calculateEndsteps();
 +
 +
function calculateEndsteps(){
 +
  finalshrink = parseInt(circleradius*0.15);
 +
  endstep1 = (cycircle+linelength+circleradius+0.1*deviceheight);
 +
  endstep2 = endstep1+0.25*deviceheight;;
 +
  endstep3 = endstep2+0.30*deviceheight;
 +
  endstep4 = (endstep3+0.25*deviceheight);
 +
  endstep5 = endstep4 +linelength +0.1*deviceheight;
 +
  endstep6 = parseInt(endstep5 + linelengthbottom + circleradiusbottom);
 +
}
 +
 +
function checkPosition(){
 +
  var yOffSet = window.pageYOffset;
 +
  if(and(animatinoCounter == 0, yOffSet > 0)){        //First animation-round: circle shrinks, first tip appears and circle moves to inside the device
 +
    animatinoCounter = 1;
 +
    var id = setInterval(function(){
 +
      shrink("sample",id,finalshrink);
 +
      startMovement = $("#sample").attr("r") == finalshrink;    //After every call of shrink, startMovement is refreshed to check if the trigger condition is already met.
 +
    },animationstep*3);            //The shrinking is triggered immediatly after scrolling down.
 +
 +
     
 +
 +
 +
    var id2 = setInterval(function(){
 +
      if(startMovement){
 +
        moveCircleY("sample",id2,endstep1,4);
 +
        moveCircleY("pulse",id2,endstep1,4);
 +
      }
 +
    },animationstep);            //Once the shrinking is done, both the sample and pulse start moving down.
 +
 +
    var id32 = setInterval(function(){
 +
      if(startMovement){
 +
        accu++;
 +
        pulse("pulse",accu,id32,circleradius*0.45,$("#sample3").attr("cx") >= parseInt(canvaswidth*0.1+0.3*devicewidth));  //$("#sample").attr("cy") == endstep3
 
          
 
          
−
<script type="text/javascript">
+
      }
−
     $('.dropdown').dropdown({on:'hover'});
+
    },pulsestep);            //After the shrinkage is done, the pulsing starts. Doesn't end.
−
</script>
+
   
−
     
+
    var id3 = setInterval(function(){
 +
      extendLineRight("tooltip-line1",(baserightLinelength),id3);
 +
      if($("#tooltip-line1").attr("x2") >= baserightLinelength){
 +
        appear("tip1");
 +
 
 +
      };
 +
    },animationstep);
 +
  }
 +
 
 +
  if(and(animatinoCounter == 4, yOffSet > 100) ){ //Second round of animation: circle turns white, goes down and second tip appears
 +
    animatinoCounter = 5;
 +
    var id = setInterval(function(){
 +
      moveCircleY("sample",id,endstep2,7);
 +
      if($("#sample").attr("cy") >= (cycircle+circleradius+linelength+0.20*deviceheight));{
 +
        clearcolor("sample");
 +
      }
 +
     },animationstep);
 +
 
 +
    var id2 = setInterval(function(){
 +
      moveCircleY("pulse",id2,endstep2,7);
 +
      if($("#pulse").attr("cy") >- (cycircle+circleradius+linelength+0.20*deviceheight));{
 +
        clearcolor("pulse");
 +
      }
 +
    },animationstep);
 +
 
 +
      var id3 = setInterval(function(){
 +
      extendLineRight("tooltip-line2",baserightLinelength*5+4,id3);
 +
      if($("#tooltip-line2").attr("x2") >= (baserightLinelength+4)){
 +
        appear("tip2");
 +
 
 +
      };
 +
    },Math.floor(animationstep*0.2));
 +
 
 +
  }
 +
 
 +
  if(and(animatinoCounter == 7, yOffSet > 200)){    //Third round of animations: Third tip appears and circle past the mid point and stips 3/4 of the device length
 +
    animatinoCounter = 8;
 +
    var id = setInterval(function(){
 +
      var id22;
 +
      moveCircleY("sample",id,endstep3,10);
 +
    },animationstep);
 +
 
 +
    var id2 = setInterval(function(){
 +
      moveCircleY("pulse",id2,endstep3,10);
 +
    },animationstep);
 +
 
 +
    var id3 = setInterval(function(){
 +
      extendLineRight("tooltip-line3",(baserightLinelength*2.5),id3);
 +
      if($("#tooltip-line3").attr("x2") >= baserightLinelength){
 +
        appear("tip3");
 +
 
 +
      };
 +
    },Math.floor(animationstep*0.01));
 +
  }
 +
 
 +
  if(and(animatinoCounter == 10, yOffSet > 300)){  //Fourth round of animations: circle divides into three and goes down. Fourth tip appears
 +
    animatinoCounter = 11;
 +
    $("#sample2").removeClass("invisible");
 +
    $("#sample2").addClass("myvisible");
 +
    $("#pulse2").removeClass("invisible");
 +
   
 +
   
 +
    $("#sample3").addClass("myvisible");
 +
    $("#sample3").removeClass("invisible");
 +
    $("#pulse3").removeClass("invisible");
 +
   
 +
   
 +
 
 +
    var id = setInterval(function(){
 +
      moveCircleX("sample3",id,canvaswidth*0.1+0.3*devicewidth,true,19);
 +
      moveCircleX("pulse3",id,canvaswidth*0.1+0.3*devicewidth,true,19);
 +
      moveCircleX("sample2",id,canvaswidth*0.1-0.3*devicewidth,false,19);
 +
      moveCircleX("pulse2",id,canvaswidth*0.1-0.3*devicewidth,false,19);
 
        
 
        
−
    <div class='ui clearing basic segment'></div>
 
  
−
     </div>   
+
     
−
</div>
+
     },animationstep*5);
 +
 
 +
    var hola = false
 +
    var id2 = setInterval(function(){
 +
      if( and(animatinoCounter == 19,(hola || (accu % 20) - 1 == 0 ))  ){
 +
        hola = true;
 +
        moveCircleY("sample",id2,endstep4,21);
 +
        moveCircleY("pulse",id2,endstep4,21);
 +
        moveCircleY("sample2",id2,endstep4,21);
 +
        moveCircleY("pulse2",id2,endstep4,21);
 +
        moveCircleY("sample3",id2,endstep4,21);
 +
        moveCircleY("pulse3",id2,endstep4,21);
 +
 
 +
      }
 +
    },animationstep);
 +
    var adios = false;
 +
    var id3= setInterval(function(){
 +
      if(and($("#sample2").attr("cx") <= canvaswidth*0.1-0.3*devicewidth, (adios || (accu % 20) - 1 == 0 ))){
 +
        adios =true ;
 +
 
 +
        accu++;
 +
        pulse("pulse",accu,id3,circleradius*0.45,false);
 +
        pulse("pulse2",accu, id3,circleradius*0.45,false);
 +
        pulse("pulse3",accu, id3,circleradius*0.45,false);
 +
      }
 +
    },pulsestep);
 +
 
 +
      var id3 = setInterval(function(){
 +
      extendLineRight("tooltip-line4",baserightLinelength*6,id3);
 +
      if($("#tooltip-line4").attr("x2") >= (baserightLinelength+4)){
 +
        appear("tip4");
 +
 
 +
      };
 +
    },Math.floor(animationstep*0.1));
 +
 
 +
  }
 +
 
 +
 
 +
  if(and(animatinoCounter ==21, yOffSet > 300)){      //Fifth round of animations:
 +
    animatinoCounter = 22;
 +
 
 +
    var id = setInterval(function(){
 +
      moveCircleY("sample",id,endstep5,28);
 +
      moveCircleY("pulse",id,endstep5,28);
 +
      moveCircleY("sample2",id,endstep5,28);
 +
      moveCircleY("pulse2",id,endstep5,28);
 +
      moveCircleY("sample3",id,endstep5,28);
 +
      moveCircleY("pulse3",id,endstep5,28);
 +
    },animationstep);
 +
  }
 +
 
 +
  if(and(animatinoCounter == 28, yOffSet > 300)){
 +
    animatinoCounter = 29;
 +
    var id = setInterval(function(){
 +
      moveCircleX("sample2",id,canvaswidth*0.1-0.3*devicewidth-linelengthHor+linewidth,false,33);
 +
      moveCircleX("pulse2",id,canvaswidth*0.1-0.3*devicewidth-linelengthHor+linewidth,false,33);
 +
      moveCircleX("sample3",id,canvaswidth*0.1+0.3*devicewidth+linelengthHor-linewidth,true,33);
 +
      moveCircleX("pulse3",id,canvaswidth*0.1+0.3*devicewidth+linelengthHor-linewidth,true,33);
 +
    },animationstep);
 +
 
 +
  }
 +
 
 +
  if(and(animatinoCounter == 33, yOffSet >300)){
 +
    animatinoCounter = 34;
 +
    var id = setInterval(function(){
 +
      moveCircleY("sample",id,endstep6,40);
 +
      moveCircleY("pulse",id,endstep6,40);
 +
      moveCircleY("sample2",id,endstep6,40);
 +
      moveCircleY("pulse2",id,endstep6,40);
 +
      moveCircleY("sample3",id,endstep6,40);
 +
      moveCircleY("pulse3",id,endstep6,40);
 +
    },animationstep);
 +
  }
 +
 
 +
 
 +
  if(and(animatinoCounter == 40, yOffSet > 300)){
 +
    animatinoCounter = 41;
 +
    var id = setInterval(function(){
 +
      expandNegative("sample2",id,parseInt(circleradiusbottom)+2);
 +
    },animationstep*5);
 +
 
 +
    var id2 = setInterval(function(){
 +
      if(animatinoCounter == 42){
 +
        expandPositive("sample",id2,parseInt(circleradiusbottom)+2);
 +
      }
 +
    },animationstep*5);
 +
 
 +
    var id3 = setInterval(function(){
 +
      if(animatinoCounter == 43){
 +
        expandNegative("sample3",id3,parseInt(circleradiusbottom)+2);
 +
      }
 +
    },animationstep*5);
 +
    var id4 = setInterval(function(){
 +
      extendLineRight("tooltip-line5",baserightLinelength*2+4,id4);
 +
      if($("#tooltip-line5").attr("x2") >= baserightLinelength){
 +
        appear("tip5");
 +
 
 +
      };
 +
    },Math.floor(animationstep*0.5));
 +
  }
 +
 
 +
 
 +
}
 +
 
 +
function shrink(circle, id, rfinal){
 +
  var r = parseInt($("#"+circle).attr("r"));
 +
  if(r != rfinal){
 +
    $("#"+circle).attr("r",r-1);
 +
  } else {
 +
    animatinoCounter++;
 +
    clearInterval(id);
 +
   
 +
  }
 +
}                          //This function shrinks a circle to a final radius.
 +
 
 +
 
 +
function appear(elementId){
 +
  $("#"+elementId).addClass("appear");
 +
  $("#"+elementId).removeClass("invisible");
 +
}                          //this function makes an element gradually change its opacity to 1 by adding the appear class in css and removing the invisible class. See style for class descriptions.
 +
 
 +
function extendLineRight(line,finalvalue,id){
 +
  var value = parseInt($("#"+line).attr("x2"));
 +
  if(value < finalvalue){
 +
    $("#"+line).attr("x2",value+1);
 +
  } else {
 +
    clearInterval(id);
 +
  }
 +
}                          //This function extends a line by increasing the x2 value until the final value is reached. To be used in conjuction with setInterval.
 +
 
 +
function clearcolor(circle){
 +
  $("#"+circle).addClass("white");
 +
}                          //This function changes the color of an Element to white using css transitions. See white class for class definition.
 +
 
 +
function animation(){
 +
  expand("sample");
 +
}
 +
 
 +
function expandNegative(circle,id,rfinal){
 +
  $("#"+circle).addClass("colorNegative");
 +
  var r = parseInt($("#"+circle).attr("r"));
 +
  if(r != rfinal + 1 ){
 +
   
 +
    $("#"+circle).attr("r",r+1);
 +
  } else {
 +
    animatinoCounter++;
 +
    clearInterval(id);
 +
   
 +
  }
 +
}
 +
 
 +
function expandPositive(circle,id,rfinal){
 +
  $("#"+circle).addClass("colorPositive");
 +
    var r = parseInt($("#"+circle).attr("r"));
 +
  if(r != rfinal + 1 ){
 +
   
 +
    $("#"+circle).attr("r",r+1);
 +
   
 +
  } else {
 +
    animatinoCounter++;
 +
    clearInterval(id);
 +
   
 +
 
 +
  }
 +
}
 +
 
 +
function moveCircleY(circle, id, cyfinal, setcounter){
 +
  var cy = parseInt($("#"+circle).attr("cy"));
 +
  if( cy <= cyfinal){
 +
   
 +
    $("#"+circle).attr("cy", cy+1);
 +
 
 +
  } else{
 +
    animatinoCounter = setcounter;
 +
    clearInterval(id);
 +
 
 +
   
 +
  }
 +
} //Moves a circle to cyfianl by and upon finishing clears id. Set counter is needed to propertly coordinate the animation counters so different screen sizes (which result in slightly different values) don't ruin the animation triggerin.
 +
 
 +
 
 +
 
 +
function moveCircleX(circle, id, cxfinal, plus, setcounter){
 +
 
 +
  var cx = parseInt($("#"+circle).attr("cx"));
 +
  if(plus == true){
 +
    if(cx <= cxfinal){
 +
      $("#"+circle).attr("cx",cx+1);
 +
    } else{
 +
     
 +
      animatinoCounter = setcounter;
 +
      clearInterval(id);
 +
 
 +
 
 +
    }
 +
  } else {
 +
    if(cx >= cxfinal){
 +
      $("#"+circle).attr("cx",cx-1);
 +
    } else {
 +
     
 +
      animatinoCounter = setcounter;
 +
      clearInterval(id);
 +
 
 +
    }
 +
  }
 +
 
 +
}
 +
 
 +
 
 +
function pulse(circle,accu,id,maxr,endcondition){
 +
    if(and(endcondition, ((accu % maxr) - 1 == 0))){
 +
            accu =0;
 +
                        clearInterval(id);
 +
     
 +
    } else{
 +
                        $("#"+circle).css("opacity",(1-((accu % maxr)/100)+''));
 +
      $("#"+circle).attr("r",(2 + (accu % maxr))+'');
 +
    }
 +
 
 +
}                          //This function takes a circle and changes periodically its opacity and radius. An accumualtor is needed for it to work propertly.
 +
 
 +
 
 +
function and(a, b){
 +
  return (!(!(a || a) || !(b || b)));
 +
}  //Calculates the value of a and b, because why should the && operator work?
 +
 
 +
 
 +
$sample = $("#sample");
 +
$pulse = $("#pulse");
 +
$sample2 = $("#sample2");
 +
$pulse2 = $("#pulse2");
 +
$sample3 = $("#sample3");
 +
$pulse3 = $("#pulse3");
 +
function skipAnimation(){
 +
  animatinoCounter=-99;  //Just to be sur
 +
    var id = setInterval(function(){
 +
      extendLineRight("tooltip-line1",(baserightLinelength-3),id);
 +
      if($("#tooltip-line1").attr("x1") >= baserightLinelength){
 +
        appear("tip1");
 +
 
 +
      };
 +
    },animationstep);
 +
 
 +
      var id2 = setInterval(function(){
 +
      extendLineRight("tooltip-line2",baserightLinelength*5+4,id2);
 +
      if($("#tooltip-line2").attr("x2") >= (baserightLinelength+4)){
 +
        appear("tip2");
 +
 
 +
      };
 +
    },animationstep*0.2);
 +
 
 +
    var id3 = setInterval(function(){
 +
      extendLineRight("tooltip-line3",(baserightLinelength*2.5-3),id3);
 +
      if($("#tooltip-line3").attr("x2") >= baserightLinelength){
 +
        appear("tip3");
 +
 
 +
      };
 +
    },animationstep*0.4);
 +
 
 +
      var id4 = setInterval(function(){
 +
      extendLineRight("tooltip-line4",baserightLinelength*6+4,id4);
 +
      if($("#tooltip-line4").attr("x2") >= (baserightLinelength+4)){
 +
        appear("tip4");
 +
 
 +
      };
 +
    },animationstep*0.1);
 +
 
 +
    var id5 = setInterval(function(){
 +
      extendLineRight("tooltip-line5",baserightLinelength*2,id5);
 +
      if($("#tooltip-line5").attr("x2") >= baserightLinelength){
 +
        appear("tip5");
 +
 
 +
      };
 +
    },animationstep*0.5);
 +
 
 +
   
 +
 
 +
    $sample.attr("cy",endstep6);
 +
    $sample.attr("cx",canvaswidth*0.1)
 +
    $sample.removeClass("white");
 +
    $sample.css("fill","rgb(100,255,0)");
 +
    $sample.attr("r",circleradiusbottom+1);
 +
    $pulse.remove();
 +
    $sample.removeAttr("id");
 +
 
 +
     
 +
    $sample2.attr("cx",parseInt(canvaswidth*0.1-0.3*devicewidth-linelengthHor+linewidth));
 +
    $sample2.attr("cy",endstep6);
 +
    $sample2.attr("r",circleradiusbottom+1);
 +
    $sample2.css("fill","rgb(0,174,239)");
 +
    $pulse2.attr("cx",parseInt(canvaswidth*0.1-0.3*devicewidth-linelengthHor+linewidth));
 +
    $pulse2.attr("cy",endstep6+2);
 +
    $sample2.removeAttr("id");
 +
    $pulse2.removeAttr("id"); //This is a patch work solution to force stop the animation when it's cancelled while the cirlces are moving horizontally. Change if needed.
 +
 
 +
 
 +
    $sample3.attr("cx",parseInt(canvaswidth*0.1+0.3*devicewidth+linelengthHor-linewidth));
 +
    $sample3.attr("cy",endstep6);
 +
    $sample3.attr("r",circleradiusbottom+1)
 +
    $sample3.css("fill","rgb(0,174,239)");
 +
    $pulse3.attr("cx",parseInt(canvaswidth*0.1+0.3*devicewidth+linelengthHor-linewidth));
 +
    $pulse3.attr("cy",endstep6+2);
 +
    $pulse3.removeAttr("id");
 +
    $sample3.removeAttr("id"); //This is a patch work solution to force stop the animation when it's cancelled while the cirlces are moving horizontally. Change if needed.
 +
    $(".sample").css("opacity","1");
 +
  }
 +
 
 +
 
 +
 
 +
var id = setInterval(function() { 
 +
  if(and($(window).scrollTop() + $(window).height() == $(document).height(),animatinoCounter >=21)) {
 +
      checkPosition();
 +
  }
 +
},100);    //This part here makes it so the animation continues without the need to scroll if the view port is at the bottom of the document.
 +
 
 +
    </script>
 +
    <script>
 +
 
 +
 
 +
$('.dropdown').dropdown({on:'hover',
 +
                    action: 'nothing'
 +
                          });
 +
  $('.ui.accordion')
 +
    .accordion()
 +
  ;
 +
 
 +
  // Create a lightbox
 +
  (function() {
 +
    var $lightbox = $("<div class='lightbox'></div>");
 +
    var $container = $("<div class='lightboxContainer'</div>");
 +
    var $img = $("<img>");
 +
    var $caption = $("<p class='caption'></p>");
 +
 
 +
    // Add image and caption to lightbox
 +
 
 +
    $container
 +
      .append($img)
 +
      .append($caption);
 +
 
 +
    $lightbox
 +
      .append($container);
 +
 
 +
    // Add lighbox to document
 +
 
 +
    $('body').append($lightbox);
 +
 
 +
    $('.lightboxAble').parent().click(function(e) {
 +
      e.preventDefault();
 +
 
 +
      // Get image link and description
 +
      var $imgelement = $(this).children("img");
 +
 
 +
      var src = $imgelement.attr("src");
 +
      var cap = $imgelement.attr("alt");
 +
      // Add data to lighbox
 +
      $img.attr('src', src);
 +
      $caption.append(cap);
 +
 
 +
      // Show lightbox
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Revision as of 13:45, 19 August 2017

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CascAID stands for Cas13a Controlled Assay for Infectious Diseases. Our goal this year is to create a novel paper-based microfluidic device for the detection of specific RNA sequences. Nowadays, there is a trend among medical practitioners to prescribe antibiotics when bacterial infections are suspected without a laboratory confirmation as a way for speeding up recovery. This has led to an increase in antibiotic-resistant bacteria that makes it difficult to treat infected patients. Nucleic acid-based detection methods could allow for faster diagnosis. Therefore, we seek to develop a method that allows to report the presence of a specific pathogen within hours. For this reason, we will use the CRISPR effector Cas13a, which is able to target specific single-stranded RNA. This system allows for the simple and fast design of new sequence targets, being an ideal tool for detecting fast mutating pathogens. In the long term, we see our device as an easy-to-use and fast diagnostic tool in developing countries as well as an instrument in developed countries for discerning between bacterial and viral infections, that could help reducing antibiotics prescription.