Difference between revisions of "Team:Munich"

Revision as of 17:02, 24 August 2017

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</head> <body onresize="renderDevice();calculateEndsteps();skipAnimation()">

           <img class="ui cascaid image" src="">

           <img class="ui cascaid image" src="">

           <img class="ui cascaid image" src="">

           Tablet

               <a class="active item">Description</a>
               <a class="disabled item">Interlab</a>

   <img class="myImg introImg" src=""/ alt="intro Picture">

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.

</section>

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     <circle class="invisible sample"  fill="white" id="sample2" />

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     <circle class="invisible sample"  fill="white" id="sample3" />

     <line class="tooltip-line" id="tooltip-line1" />  
   </svg>

     <img class="pretty-picture lightboxAble" src="" alt="Step 1:

     A sample, such as blood or saliva, is placed into the device.">

Step 1:
A sample, such as blood or saliva, is placed into the device.

     <img class="pretty-picture lightboxAble" src="">

Step 3:
Cas13a binds the target sequence and cuts it in smaller fragments. After this inital digestion, the enzyme changes into a RNAase-active conformation.

     <img class="pretty-picture" src="">

Step 5:
An easy to interpret read-out tells whether a specific pathogen was present in the sample.

       <img class="pretty-picture lightboxAble" src="">

Step 2:
RNA is purified with the help of our reusable, 3D-printed microfluidic device.

       <img class="pretty-picture lightboxAble" src="">

Step 4:
While in this conformation, Cas13a degrades the read-out RNA, producing a visible signal.

 <a class="item" href="https://www.facebook.com/Munich.iGEM/">
   
 </a>
 <a class="item" href="https://www.instagram.com/igem.munich.2017/">
   
 </a>
 <a class="item" href="mailto:igem.munich@gmail.com">
   
 </a>

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   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);

   },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() >= 0.9,animatinoCounter >0)) {
      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 = $(""); var $container = $("<div class='lightboxContainer'

");

   var $img = $("<img>");

var $caption = $("

");

   // 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

     $lightbox.fadeIn('fast');

     $lightbox.click(function() {
       $lightbox.fadeOut('fast', function(){
         $caption.empty();
       });
     });
   });

 }());
   </script>

</body>

Revision as of 13:05, 23 August 2017 (view source) Jorge Quintero (Talk \| contribs) ← Older edit		Revision as of 17:02, 24 August 2017 (view source) Jorge Quintero (Talk \| contribs) Newer edit →
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−	~~<html>~~
	<head>		<head>