Difference between revisions of "Team:Fudan-TSI/Composite Part"

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{{Fudan-TSI}}<script src="https://ajax.aspnetcdn.com/ajax/jQuery/jquery-1.11.3.min.js"></script>
+
{{Fudan-TSI}}<!-- jquery loaded by HQ 1.12.4 -->
<html lang="en">
+
<html></p></div></div></div><meta name="viewport" content="width=device-width, initial-scale=1"><meta charset="UTF-8">
<!--
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  <link rel="stylesheet" href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/materialize.css&action=raw&ctype=text/css">
This html document is created by Tian Huang for Team Fudan iGEM 2018.
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  <link rel="stylesheet" href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/Fudan-font-awesome.css&action=raw&ctype=text/css" />
We make it compatible on laptop and mobile devices by using Materialize 1.0.0-rc.2.
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  <link rel="stylesheet" type="text/css" href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/Fudan-css.css&action=raw&ctype=text/css" />
-->
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<style>
<!-- LC check on 2018-10-18 -->
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/*****************************************************************************/
<head>
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/* DEFAULT WIKI SETTINGS */
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/*****************************************************************************/
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  #home_logo, #sideMenu { display:none; }
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  #sideMenu, #top_title, .patrollink { display:none; }
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  #content { margin-left: 0; padding:0px; width:100%;}
 +
  .judges-will-not-evaluate { border: 4px solid #e4dede; padding: 2% !important; width: 92%!important; }
 +
/* css clean * */
 +
  #FudanTSIBody li { list-style: none; }
 +
    </style>
 +
    <title>Composite Parts | 2019 iGEM Team:Fudan-TSI</title>
 +
</head>
 +
<body>
 +
<div id="FudanTSIdivWrapper"><div id="FudanTSIBody">
 +
  <header>
 +
  <div id="emptyBar" style="position:relative;width: 100%;"></div><nav id="topNav" class="black z-depth-0_5"><div class="nav-wrapper"><div id="teamLogo" class="brand-logo"> <a href="/Team:Fudan-TSI" target="_self"><img alt="2019 team logo" src="https://static.igem.org/mediawiki/2019/d/d3/T--Fudan-TSI--HomepageLogo.gif"></a></div><ul id="nav-mobile" class="right">
 +
    <li class="hide-on-med-and-down"><a class="dropdown-trigger" data-target="dropdown1">Project</a></li><li class="hide-on-med-and-down"><a class="dropdown-trigger" data-target="dropdown2">Results</a></li><li class="hide-on-med-and-down"><a class="dropdown-trigger" data-target="dropdown3">Model</a></li><li class="hide-on-med-and-down"><a class="dropdown-trigger" data-target="dropdown4">Parts</a></li><li class="hide-on-med-and-down"><a class="dropdown-trigger" data-target="dropdown5">Human&nbsp;practices</a></li><li class="hide-on-med-and-down"><a class="dropdown-trigger" data-target="dropdown6">Team</a></li>
 +
    <li class="hide-on-med-and-down"><a href="/Team:Fudan-TSI/Judging">Judging</a></li>
 +
    <li> <a id="navList" data-target="slide-out" class="waves-effect waves-light sidenav-trigger right"> <i class="fa fa-navicon" style="font-size: 24px"></i> </a></li></ul></div> </nav>
 +
  <!-- Dropdown and List elements in navigation bar -->
 +
  <ul id="dropdown1" class="dropdown-content">
 +
      <li><a href="/Team:Fudan-TSI/Description">Background</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Design">Design</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Experiments">Experiments</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Applied_Design">Applied&nbsp;design</a></li>
 +
  </ul>
 +
  <ul id="dropdown2" class="dropdown-content">
 +
      <li><a href="/Team:Fudan-TSI/Demonstrate#ReverseTranscription">Reverse&nbsp;transcription</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Demonstrate#Recombination">Recombination</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Demonstrate">Demonstration</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Measurement">Measurement</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Notebook">Notebook</a></li>
 +
  </ul>
 +
  <ul id="dropdown3" class="dropdown-content">
 +
      <li><a href="/Team:Fudan-TSI/Model">Modeling</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Software">Software</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Hardware">Hardware</a></li>
 +
  </ul>
 +
  <ul id="dropdown4" class="dropdown-content">
 +
      <li><a href="/Team:Fudan-TSI/Basic_Part">Basic&nbsp;parts</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Composite_Part">Composite&nbsp;parts</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Improve">Part&nbsp;improvement</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Part_Collection">Part&nbsp;collection</a></li>
 +
  </ul>
 +
  <ul id="dropdown5" class="dropdown-content">
 +
      <li><a href="/Team:Fudan-TSI/Public_Engagement">Public&nbsp;engagement</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Human_Practices#IntegratedHumanPractice">Integrated&nbsp;HP</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Collaborations">Collaborations</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Safety">Safety</a></li>
 +
  </ul>
 +
  <ul id="dropdown6" class="dropdown-content">
 +
      <li><a href="/Team:Fudan-TSI/Team">Members</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Attributions">Attributions</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Team#Acknowledge">Acknowledge</a></li>
 +
      <li><a href="/Team:Fudan-TSI/Heritage">Heritage</a></li>
 +
  </ul>
  
    <!-- CSS -->
 
    <link rel="stylesheet" type="text/css" href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/Fudan-css.css&action=raw&ctype=text/css" />
 
  
    <!-- Font-awesome icons 4.7.0 -->
+
  <ul id="slide-out" class="sidenav">
     <link href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/Fudan-font-awesome.css&action=raw&ctype=text/css" rel="stylesheet" />
+
    <li style="padding: 0"><div class="sidenavBanner">
 +
      <div class="background"></div>
 +
      <p class="flow-text" style="width:100%;text-align:center"><span class="white-text">Composite Parts</span></p>
 +
     </div></li>
 +
    <li>
 +
      <ul class="collapsible expandable">
 +
        <li><span class="pageSidebar">Team: Fudan-TSI</span></li><li><div class="collapsible-header"><span class="pageSidebar">Project</span></div><div class="collapsible-body"><ul><li><a class="pageSidebar" href="/Team:Fudan-TSI/Description">Background</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Design">Design</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Experiments">Experiments</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Applied_Design">Applied design</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Judging">Judging</a></li></ul></div></li><li><div class="collapsible-header"><span class="pageSidebar">Results</span></div><div class="collapsible-body"><ul><li><a class="pageSidebar" href="/Team:Fudan-TSI/Demonstrate#ReverseTranscription">Reverse transcription</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Demonstrate#Recombination">Recombination</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Demonstrate">Demonstration</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Measurement">Measurement</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Notebook">Notebook</a></li></ul></div></li><li><div class="collapsible-header"><span class="pageSidebar">Model</span></div><div class="collapsible-body"><ul><li><a class="pageSidebar" href="/Team:Fudan-TSI/Model">Modeling</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Software">Software</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Hardware">Hardware</a></li></ul></div></li><li><div class="collapsible-header active"><span class="pageSidebar">Parts</span></div><div class="collapsible-body"><ul><li><a class="pageSidebar" href="/Team:Fudan-TSI/Basic_Part">Basic parts</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Composite_Part">Composite parts</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Improve">Part improvement</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Part_Collection">Part collection</a></li></ul></div></li><li><div class="collapsible-header"><span class="pageSidebar">Human practices</span></div><div class="collapsible-body"><ul><li><a class="pageSidebar" href="/Team:Fudan-TSI/Public_Engagement">Public engagement</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Human_Practices#IntegratedHumanPractice">Integrated HP</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Collaborations">Collaborations</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Safety">Safety</a></li></ul></div></li><li><div class="collapsible-header"><span class="pageSidebar">Team</span></div><div class="collapsible-body"><ul><li><a class="pageSidebar" href="/Team:Fudan-TSI/Team">Members</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Attributions">Attributions</a></li><li><a class="pageSidebar" href="/Team:Fudan-TSI/Heritage">Heritage</a></li></ul></div></li>
 +
      </ul><!-- .expandable -->
 +
    </li>
 +
    <li><div class="placeHolder"></div></li>
 +
  </ul>
 +
  </header>
  
    <!-- Materialize 1.0.0-rc.2 (Material Design like) -->
+
  <div id="pageContent">
    <link rel="stylesheet" href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/materialize.css&action=raw&ctype=text/css">
+
      <div id="contentBanner" class="figureBanner">
 +
          <div class="row">
 +
              <div class="col s12 hide-on-med-and-up">
 +
                  <h1><br/>Composite Parts</h1>
 +
              </div>
 +
          </div>
 +
          <div class="hide-on-small-only">
 +
<style>
 +
#demo {width:100%;height:100%;position:relative;z-index:-100;}
 +
#demo svg {width:100%;height:100%;position:fixed;}
 +
#demo svg g {mix-blend-mode:lighten;}
 +
#demo svg polygon {stroke:none;fill:white;}
 +
</style>
 +
<div id="pageCover">
 +
  <svg id="demo" viewBox="0 0 1600 600" preserveAspectRatio="xMidYMid slice">
 +
        <defs>
 +
        <linearGradient id="grad1" x1="0" y1="0" x2="1" y2="0" color-interpolation="sRGB">
 +
          <stop id="stop1a" offset="0%" stop-color="#12a3b4"></stop>
 +
          <stop id="stop1b" offset="100%" stop-color="#ff509e"></stop>
 +
        </linearGradient>
 +
        <linearGradient id="grad2" x1="0" y1="0" x2="1" y2="0" color-interpolation="sRGB">
 +
          <stop id="stop2a" offset="0%" stop-color="#e3bc13"></stop>
 +
          <stop id="stop2b" offset="100%" stop-color="#00a78f"></stop>
 +
        </linearGradient>
 +
        </defs>
 +
        <rect id="rect1" x="0" y="0" width="1600" height="600" stroke="none" fill="url(#grad1)"></rect>
 +
        <rect id="rect2" x="0" y="0" width="1600" height="600" stroke="none" fill="url(#grad2)"></rect>
 +
  </svg>
 +
</div><!-- #pageCover -->
 +
<script src="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/bkg&action=raw&ctype=text/javascript"></script>
 +
        <script>
 +
      //////////////////////////////
 +
      // Demo Functions
 +
      //////////////////////////////
 +
      function bkgFunction(showStats) {
 +
        // stats
 +
        if (showStats) {
 +
        var stats = new Stats();
 +
        stats.domElement.style.position = 'absolute';
 +
        stats.domElement.style.left = '0';
 +
        stats.domElement.style.top = '0';
 +
        document.body.appendChild(stats.domElement);
 +
        requestAnimationFrame(function updateStats(){
 +
          stats.update();
 +
          requestAnimationFrame(updateStats);
 +
        });
 +
        }
 +
        // init
 +
        var svg = document.getElementById('demo');
 +
        tesselation.setup(svg);
 +
        gradients.setup();
 +
        var lastTransitionAt, transitionDelay = 10000, transitionDuration = 3000;
 +
        function playNextTransition() {
 +
        tesselation.next(transitionDuration);
 +
        gradients.next(transitionDuration);
 +
        };
 +
        function tick(time) {
 +
        if (!lastTransitionAt || time - lastTransitionAt > transitionDelay) {
 +
          lastTransitionAt = time;
 +
          playNextTransition();
 +
        }
 +
        window.requestAnimationFrame(tick);
 +
        }
 +
        window.requestAnimationFrame(tick);
 +
      }
 +
      //////////////////////////////
 +
      // Delaunay Triangulation
 +
      //////////////////////////////
 +
      var calcDelaunayTriangulation = (function() {
 +
        var EPSILON = 1.0 / 1048576.0;
 +
        function getSuperT(vertices) {
 +
        var xMin = Number.POSITIVE_INFINITY, yMin = Number.POSITIVE_INFINITY,
 +
          xMax = Number.NEGATIVE_INFINITY, yMax = Number.NEGATIVE_INFINITY,
 +
          i, xDiff, yDiff, maxDiff, xCenter, yCenter;
 +
        for(i = vertices.length; i--; ) {
 +
          if(vertices[i][0] < xMin) xMin = vertices[i][0];
 +
          if(vertices[i][0] > xMax) xMax = vertices[i][0];
 +
          if(vertices[i][1] < yMin) yMin = vertices[i][1];
 +
          if(vertices[i][1] > yMax) yMax = vertices[i][1];
 +
        }
 +
        xDiff = xMax - xMin;
 +
        yDiff = yMax - yMin;
 +
        maxDiff = Math.max(xDiff, yDiff);
 +
        xCenter = xMin + xDiff * 0.5;
 +
        yCenter = yMin + yDiff * 0.5;
 +
        return [
 +
          [xCenter - 20 * maxDiff, yCenter - maxDiff],
 +
          [xCenter, yCenter + 20 * maxDiff],
 +
          [xCenter + 20 * maxDiff, yCenter - maxDiff]
 +
        ];
 +
        }
 +
        function circumcircle(vertices, i, j, k) {
 +
        var xI = vertices[i][0], yI = vertices[i][1],
 +
          xJ = vertices[j][0], yJ = vertices[j][1],
 +
          xK = vertices[k][0], yK = vertices[k][1],
 +
          yDiffIJ = Math.abs(yI - yJ), yDiffJK = Math.abs(yJ - yK),
 +
          xCenter, yCenter, m1, m2, xMidIJ, xMidJK, yMidIJ, yMidJK, xDiff, yDiff;
 +
        // bail condition
 +
        if(yDiffIJ < EPSILON){
 +
          if (yDiffJK < EPSILON){
 +
            throw new Error("Can't get circumcircle since all 3 points are y-aligned");
 +
          }
 +
        }
  
    <!-- Clear default CSS settings; CSS reset -->
 
    <style>
 
        *{margin: 0;padding: 0;list-style: none;}
 
        /* via: https://blog.csdn.net/weixin_41014370/article/details/79523637 */
 
  
         /** 清除内外边距 **/
+
         // calc circumcircle center x/y, radius
         body, h1, h3, h3, h4, h5, h6, hr, p, blockquote, /* structural elements 结构元素 */
+
         m1  = -((xJ - xI) / (yJ - yI));
         dl, dt, dd, ul, ol, li, /* list elements 列表元素 */
+
        m2  = -((xK - xJ) / (yK - yJ));
         pre, /* text formatting elements 文本格式元素 */
+
         xMidIJ = (xI + xJ) / 2.0;
         form, fieldset, legend, button, input, textarea, /* form elements 表单元素 */
+
        xMidJK = (xJ + xK) / 2.0;
         th, td /* table elements 表格元素 */ {
+
         yMidIJ = (yI + yJ) / 2.0;
            margin: 0;
+
         yMidJK = (yJ + yK) / 2.0;
            padding: 0;
+
        xCenter = (yDiffIJ < EPSILON) ? xMidIJ :
 +
          (yDiffJK < EPSILON) ? xMidJK :
 +
          (m1 * xMidIJ - m2 * xMidJK + yMidJK - yMidIJ) / (m1 - m2);
 +
         yCenter  = (yDiffIJ > yDiffJK) ?
 +
          m1 * (xCenter - xMidIJ) + yMidIJ :
 +
          m2 * (xCenter - xMidJK) + yMidJK;
 +
        xDiff = xJ - xCenter;
 +
        yDiff = yJ - yCenter;
 +
        // return
 +
        return {i: i, j: j, k: k, x: xCenter, y: yCenter, r: xDiff * xDiff + yDiff * yDiff};
 
         }
 
         }
 +
        function dedupeEdges(edges) {
 +
        var i, j, a, b, m, n;
 +
        for(j = edges.length; j; ) {
 +
          b = edges[--j]; a = edges[--j];
 +
          for(i = j; i; ) {
 +
          n = edges[--i]; m = edges[--i];
 +
          if(a === m){
 +
            if (b===n){
 +
              edges.splice(j, 2); edges.splice(i, 2);
 +
              break;
 +
            }
 +
          }
 +
          if(a === n){
 +
            if (b===m){
 +
              edges.splice(j, 2); edges.splice(i, 2);
 +
              break;
 +
            }
 +
          }
 +
          }
 +
        }
 +
        }
 +
        return function(vertices) {
 +
        var n = vertices.length,
 +
          i, j, indices, st, candidates, locked, edges, dx, dy, a, b, c;
 +
        // bail if too few / too many verts
 +
        if(n < 3 || n > 2000)
 +
          return [];
 +
        // copy verts and sort indices by x-position
 +
        vertices = vertices.slice(0);
 +
        indices = new Array(n);
 +
        for(i = n; i--; )
 +
          indices[i] = i;
 +
        indices.sort(function(i, j) {
 +
          return vertices[j][0] - vertices[i][0];
 +
        });
 +
        // supertriangle
 +
        st = getSuperT(vertices);
 +
        vertices.push(st[0], st[1], st[2]);
 +
        // init candidates/locked tris list
 +
        candidates = [circumcircle(vertices, n + 0, n + 1, n + 2)];
 +
        locked = [];
 +
        edges = [];
 +
        // scan left to right
 +
        for(i = indices.length; i--; edges.length = 0) {
 +
          c = indices[i];
 +
          // check candidates tris against point
 +
          for(j = candidates.length; j--; ) {
 +
          // lock tri if point to right of circumcirc
 +
          dx = vertices[c][0] - candidates[j].x;
 +
          if (dx > 0.0){
 +
            if(dx * dx > candidates[j].r){
 +
              locked.push(candidates[j]);
 +
            candidates.splice(j, 1);
 +
            continue;
 +
            }
 +
          }
  
        /** 设置默认字体 **/
 
  
        h1, h3, h3, h4, h5, h6 { font-size: 100%; }
+
          // point outside circumcirc = leave candidates
        address, cite, dfn, em, var { font-style: normal; } /* 将斜体扶正 */
+
          dy = vertices[c][1] - candidates[j].y;
        code, kbd, pre, samp { font-family: courier new, courier, monospace; } /* 统一等宽字体 */
+
          if(dx * dx + dy * dy - candidates[j].r > EPSILON)
         small { font-size: 12px; } /* 小于 12px 的中文很难阅读,让 small 正常化 */
+
            continue;
 +
          // point inside circumcirc = break apart, save edges
 +
          edges.push(
 +
            candidates[j].i, candidates[j].j,
 +
            candidates[j].j, candidates[j].k,
 +
            candidates[j].k, candidates[j].i
 +
          );
 +
          candidates.splice(j, 1);
 +
          }
 +
          // new candidates from broken edges
 +
          dedupeEdges(edges);
 +
          for(j = edges.length; j; ) {
 +
          b = edges[--j];
 +
          a = edges[--j];
 +
          candidates.push(circumcircle(vertices, a, b, c));
 +
          }
 +
        }
 +
        // close candidates tris, remove tris touching supertri verts
 +
         for(i = candidates.length; i--; )
 +
          locked.push(candidates[i]);
 +
        candidates.length = 0;
 +
        for(i = locked.length; i--; )
 +
          if(locked[i].i < n){
 +
            if(locked[i].j < n){
 +
              if(locked[i].k < n){
 +
                candidates.push(locked[i].i, locked[i].j, locked[i].k);
 +
              }
 +
            }
 +
          }
  
        /** 重置列表元素 **/
 
        ul, ol { list-style: none; }
 
  
         /** 重置文本格式元素 **/
+
         // done
         a { text-decoration: none; }
+
        return candidates;
         a:hover { text-decoration: underline; }
+
        };
 +
      })();
 +
      var tesselation = (function() {
 +
        var svg, svgW, svgH, prevGroup;
 +
        function createRandomTesselation() {
 +
        var wW = window.innerWidth;
 +
        var wH = window.innerHeight;
 +
        var gridSpacing = 250, scatterAmount = 0.75;
 +
        var gridSize, i, x, y;
 +
        if (wW / wH > svgW / svgH) { // window wider than svg = use width for gridSize
 +
          gridSize = gridSpacing * svgW / wW;
 +
        } else { // window taller than svg = use height for gridSize
 +
          gridSize = gridSpacing * svgH / wH;
 +
        }
 +
        var vertices = [];
 +
        var xOffset = (svgW % gridSize) / 2, yOffset = (svgH % gridSize) / 2;
 +
        for (x = Math.floor(svgW/gridSize) + 1; x >= -1; x--) {
 +
          for (y = Math.floor(svgH/gridSize) + 1; y >= -1; y--) {
 +
          vertices.push(
 +
            [
 +
            xOffset + gridSize * (x + scatterAmount * (Math.random() - 0.5)),
 +
            yOffset + gridSize * (y + scatterAmount * (Math.random() - 0.5))
 +
            ]
 +
          );
 +
          }
 +
        }
 +
        var triangles = calcDelaunayTriangulation(vertices);
 +
        var group = document.createElementNS('http://www.w3.org/2000/svg','g');
 +
         var polygon;
 +
        for(i = triangles.length; i; ) {
 +
          polygon = document.createElementNS('http://www.w3.org/2000/svg','polygon');
 +
          polygon.setAttribute('points',
 +
          vertices[triangles[--i]][0] + ',' + vertices[triangles[i]][1] + ' ' +
 +
          vertices[triangles[--i]][0] + ',' + vertices[triangles[i]][1] + ' ' +
 +
          vertices[triangles[--i]][0] + ',' + vertices[triangles[i]][1]
 +
          );
 +
          group.appendChild(polygon);
 +
        }
 +
        return group;
 +
        }
 +
        return {
 +
        setup: function(svgElement) {
 +
          svg = svgElement;
 +
          var vb = svg.getAttribute('viewBox').split(/\D/g);
 +
          svgW = vb[2];
 +
          svgH = vb[3];
 +
        },
 +
         next: function(t) {
 +
          var toRemove, i, n;
 +
          t /= 1000;
 +
          if(prevGroup){
 +
            if(prevGroup.children){
 +
              if(prevGroup.children.length){
 +
                toRemove = prevGroup;
 +
                n = toRemove.children.length;
 +
                for (i = n; i--; ) {
 +
                  TweenMax.to(toRemove.children[i], t*0.4, {opacity: 0, delay: t*(0.3*i/n)});
 +
                }
 +
                TweenMax.delayedCall(t * (0.7 + 0.05), function(group) { svg.removeChild(group); }, [toRemove], this);
 +
              }
 +
            }
 +
          }
  
 +
          var g = createRandomTesselation();
 +
          n = g.children.length;
 +
          for (i = n; i--; ) {
 +
          TweenMax.fromTo(g.children[i], t*0.4, {opacity: 0}, {opacity: 0.3 + 0.25 * Math.random(), delay: t*(0.3*i/n + 0.3), ease: Back.easeOut});
 +
          }
 +
          svg.appendChild(g);
 +
          prevGroup = g;
 +
        }
 +
        }
 +
      })();
 +
      //////////////////////////////
 +
      // Gradients
 +
      //////////////////////////////
 +
      var gradients = (function() {
 +
        var grad1, grad2, showingGrad1;
 +
        // using colors from IBM Design Colors this time
 +
        var colors = [ // 14 colors - use 3-5 span
 +
        '#3c6df0', // ultramarine50
 +
        '#12a3b4', // aqua40
 +
        '#00a78f', // teal40
 +
        '#00aa5e', // green40
 +
        '#81b532', // lime30
 +
        '#e3bc13', // yellow20
 +
        '#ffb000', // gold20
 +
        '#fe8500', // orange30
 +
        '#fe6100', // peach40
 +
        '#e62325', // red50
 +
        '#dc267f', // magenta50
 +
        '#c22dd5', // purple50
 +
        '#9753e1', // violet50
 +
        '#5a3ec8'  // indigo60
 +
        ];
 +
        function assignRandomColors(gradObj) {
 +
        var rA = Math.floor(colors.length * Math.random());
 +
        var rB = Math.floor(Math.random() * 3) + 3; // [3 - 5]
 +
        rB = (rA + (rB * (Math.random() < 0.5 ? -1 : 1)) + colors.length) % colors.length;
 +
        gradObj.stopA.setAttribute('stop-color', colors[rA]);
 +
        gradObj.stopB.setAttribute('stop-color', colors[rB]);
 +
        }
 +
        return {
 +
        setup: function() {
 +
          showingGrad1 = false;
 +
          grad1 = {
 +
          stopA: document.getElementById('stop1a'),
 +
          stopB: document.getElementById('stop1b'),
 +
          rect:  document.getElementById('rect1')
 +
          };
 +
          grad2 = {
 +
          stopA: document.getElementById('stop2a'),
 +
          stopB: document.getElementById('stop2b'),
 +
          rect:  document.getElementById('rect2')
 +
          };
 +
          grad1.rect.style.opacity = 0;
 +
          grad2.rect.style.opacity = 0;
 +
        },
 +
        next: function(t) {
 +
          t /= 1000;
 +
          var show, hide;
 +
          if (showingGrad1) {
 +
          hide = grad1;
 +
          show = grad2;
 +
          } else {
 +
          hide = grad2;
 +
          show = grad1;
 +
          }
 +
          showingGrad1 = !showingGrad1;
 +
          TweenMax.to(hide.rect, 0.55*t, {opacity: 0, delay: 0.2*t, ease: Sine.easeOut});
 +
          assignRandomColors(show);
 +
          TweenMax.to(show.rect, 0.65*t, {opacity: 1, ease: Sine.easeIn});
 +
        }
 +
        };
 +
      })();
 +
      //////////////////////////////
 +
      // Start
 +
      //////////////////////////////
 +
      bkgFunction();
 +
    </script>
 +
              <div style="position:absolute;top:100px;left:9%"><center><img style="height:120px;width:auto" alt="cover gif 1st added" src="https://static.igem.org/mediawiki/2019/e/ee/T--Fudan-TSI--coverCompositeParts.gif" /></center></div>
 +
          </div>
 +
      </div>
  
        /** 重置表单元素 **/
+
<!--////////////////////////////////////////////////////
        legend { color: #000; } /* for ie6 */
+
      do not edit above, if must BE CAREFUL
        fieldset, img { border: 0; } /* img 搭车:让链接里的 img 无边框 */
+
  //////////////////////////////////////////////////////-->
        button, input, select, textarea { font-size: 100%; } /* 使得表单元素在 ie 下能继承字体大小 */
+
      <div class="container">
        /* 注:optgroup 无法扶正 */
+
          <!-- side navigator of page content -->
 +
          <!-- main content of the page -->
 +
          <main style="margin:0"><article>
  
        /** 重置表格元素 **/
+
<div class="section container">
        table { border-collapse: collapse; border-spacing: 0; }
+
  <p class="flow-text">For best composite part, we would like to present you with our <a href="/Team:Fudan-TSI/Part_Collection">Cre recombinase together with degradation tag</a>. Cre recombinase <a href="http://parts.igem.org/Part:BBa_K3257044" target="_blank">(BBa_K3257044)</a> is responsible for the recombination process between the reverse transcribed cDNA and the target Gene of Interest (GOI), which is rather one of the most important processes in our system.</p>
    </style>
+
  <p class="flow-text">Because of the leakage of uninduced Cre expression, we have spent much effort in lowering the steady-state expression level of Cre. An important approach is to attach 5 different types of degradation tags after the CDS of Cre. Using EGFP <a href="http://parts.igem.org/Part:BBa_E0040" target="_blank">(BBa_E0040)</a> as a reporter, we can see that the degradation rate of degradation tag with amino acid residual sequence of AANDENWVLAA <a href="http://parts.igem.org/Part:BBa_K3257073" target="_blank">(BBa_K3257073)</a> is moderate for Cre recombinase to reach a steady but relatively low level of expression <a href="#Fig1">(Figure 1)</a>.</p>
    <title>2019 Team:Fudan -Composite_Part</title>
+
</head>
+
  
<body>
+
  <div class="figureHolder" id="Fig1">
<!-- Fudan div at igem.org -->
+
     <img class="responsive-img" src="https://static.igem.org/mediawiki/2019/3/34/T--Fudan-TSI--Composite_Fig1.png" />
<div id="FudanWrapper" class="white">
+
    <p><b>Figure 1. Degradation tag greatly reduces the protein level at stable state.</b><br/>
     <div id="FudanBody" class="white">
+
    WT represents the positive control of EGFP without any tag attachment. The five degradation tags are represented by their last five amino acid sequence. The vertical axe shows the quantitative analysis of EGFP fluorescence (excitation wavelength: 485 nm; detection wavelength: 528 nm), normalized by cell amount (OD600). The fluorescence is quantified by the concentration of green fluorescein, cell number is quantified by the number of silicon beads, both are from the distributed measurement kit. Fluorescence below detection level are eliminated. Error bar stands for the SEM of 3 replicates. t-test is performed between WT and each degradation tag, P<0.0001 (****).</p>
        <header>
+
  </div>
            <!-- empty bar -->
+
            <div id="emptyBar" style="position:relative;width: 100%;"></div>
+
  
            <!-- Navigation bar -->
+
  <p class="flow-text">Transformed into BL21(DE3) with another plasmid containing lox sites and analyzed by colony PCR, we can see that DNA cleavage between identical-oriented loxP sites happens indicating the normal function of Cre recombinase <a href="#Fig2">(Figure 2)</a>. For more information of other composite parts, please refer to <a href="/Team:Fudan-TSI/Part_Collection">the part collection page</a> and <a target="_blank" href="http://parts.igem.org/">the iGEM Part Registry</a> ranging from BBa_K3257100 to BBa_K3257118.</p>
            <!-- Dropdown and List elements in navigation bar -->
+
            <!-- Slide-out navigator contents -->
+
        </header>
+
  
        <div id="pageContent" style="">
+
  <div align="center" class="figureHolder" id="Fig2">
            <div id="contentBanner" class="figureBanner">
+
    <img class="responsive-img" src="https://static.igem.org/mediawiki/2019/9/97/T--Fudan-TSI--Composite_Fig2.gif" />
                <div class="row">
+
    <p><b>Figure 2. The verification of DNA cleavage between LoxP sites.</b><br/>
                    <div class="col s12 m6 valign-wrapper hide-on-med-and-up">
+
    Plasmids containing the Cre gene were co-transformed with plasmids containing mCherry flanked by LoxP sites. A pair of sequencing primers were used to amplify the mCherry gene. PCR product would be around 1000 bp while fragments cleaved by Cre recombinase would be approximately 250 bp. The positive control group is the PCR product of plasmids containing the original mCherry gene. The negative control group is the PCR product of plasmids containing the Cre gene only.</p>
                        <h1>Composite parts</h1>
+
  </div>
                    </div>
+
                    <div class="col s12 m6 valign-wrapper hide-on-med-and-up">
+
                        <span>This year, our BioBrick submission includes 7 versions of SynNotch receptors, with our favorite being &alpha;CD19-mN1c-tTAA.</span>
+
                    </div>
+
                </div>
+
                <div id="figureBannerTitle" class="hide-on-small-only">
+
                    <h1>Composite parts</h1>
+
                    <p><span>This year, our BioBrick submission includes 7 versions of SynNotch receptors, with our favorite being &alpha;CD19-mN1c-tTAA.</span></p>
+
                </div>
+
                <div class="hide-on-small-only">
+
                    <img src="https://static.igem.org/mediawiki/2018/a/ad/T--Fudan--title_composite.jpg">
+
                    <svg width="10" height="10" xmlns="http://www.w3.org/2000/svg" style="position:absolute; left:0;top:0; width: 4%;height: 100%;">
+
                        <defs>
+
                            <linearGradient y2="0%" x2="100%" y1="0%" x1="0%" id="blackgraleft">
+
                                <stop stop-color="rgb(0,0,0)" stop-opacity="1" offset="0%"/>
+
                                <stop stop-color="rgb(0,0,0)" stop-opacity="0" offset="100%"/>
+
                            </linearGradient>
+
                        </defs>
+
                        <g>
+
                            <rect id="svg_1" fill="url(#blackgraleft)" height="100%" width="100%"/>
+
                        </g>
+
                    </svg>
+
                    <svg width="10" height="10" xmlns="http://www.w3.org/2000/svg" style="position:absolute; right:0;top:0; width: 4%;height: 100%;">
+
                        <defs>
+
                            <linearGradient y2="0%" x2="100%" y1="0%" x1="0%" id="blackgraright">
+
                                <stop stop-color="rgb(0,0,0)" stop-opacity="0" offset="0%"/>
+
                                <stop stop-color="rgb(0,0,0)" stop-opacity="1" offset="100%"/>
+
                            </linearGradient>
+
                        </defs>
+
                        <g>
+
                            <rect id="svg_2" fill="url(#blackgraright)" height="100%" width="100%"/>
+
                        </g>
+
                    </svg>
+
                </div>
+
            </div>
+
  
            <!-- main content of the page -->
+
  <p class="flow-text">Combining these two results, we show that this composite part is able to express Cre recombinase which functions well in an <i>E. coli</i> cell at a relatively low expression level, which is we need for new recombinants accumulating during the R-Evolution process.</p>
            <div class="container">
+
                <main style="margin: 0">
+
                    <div class="section container">
+
                        <h2>Part:BBa_K2549021 <a href="http://parts.igem.org/Part:BBa_K2549021" target=_blank>&alpha;CD19-mN1c-tTAA</a></h2>
+
                        <h3>Introduction</h3>
+
                        <p>This year we have provided 7 versions of SynNotch receptors in our BioBrick submission, enabling others to wire their contact-dependent signal transduction in mammalian cells. Multiple combinations of extracellular domains, transmembrane core regions and intracellular domains make it even easier for others to readily assemble their own desirable genetic circuits. </p>
+
                        <p><b>Among the 7 SynNotch receptors, our favorite one is &alpha;CD19-mN1c-tTAA <a href="http://parts.igem.org/Part:BBa_K2549021" target="_blank">(BBa_K2549021)</a></b><br/>
+
<img alt="part BBa_K2549021" src="https://static.igem.org/mediawiki/2018/thumb/0/0c/T--Fudan--BBa_K2549021.png/1339px-T--Fudan--BBa_K2549021.png" />
+
</p>
+
                        <h3>How &alpha;CD19-mN1c-tTAA works
+
                        </h3>
+
                        <p>It receives ligand-dependent signal via the CD19 scFv and undergoes a cleavage process in which the tTA advance is released, then entering into the nucleus to activate the expression of TRE3GV promotor. Thus it can be served as a signal input module.
+
                        </p>
+
                        <h3>Advantages of &alpha;CD19-mN1c-tTAA
+
                        </h3>
+
                        <p>We have conducted flow cytometry experiments to test our SynNotch receptors and after testing, &alpha;CD19-mN1c-tTAA have stood out for showing the highest signal-to-noise ratio. We have also discovered that it has the highest activation ratio when activated by surface-expressed CD19 antigen. Moreover, it also shows only a few amount of false activation which can be tolerated. As it performs great modularity and has a great potential to be utilized by others to assemble their own CD19-dependent signal transduction module, this especially enables the possibility of the clinical application of SynNotch receptors.
+
                        </p>
+
                        <div class="figureHolder width40" style="margin: 23px auto 0 auto;">
+
                            <img class="responsive-img" src="https://static.igem.org/mediawiki/2018/b/bc/T--Fudan--composite-1.png">
+
  
                        </div>
+
  <p class="flow-text">In the future, iGEMers and synthetic biologists may use this part for homologous recombination with different degradation tags and promoters based on their own requirements.</p>
                        <p style="margin-top:0;text-indent: 0;"><b>Figure 1. Flow cytometry characterization of SynNotch receptors.</b> TRE3GV-EGFP circuit was set to indicate the activation level of SynNotch receptors. It is shown that &alpha;CD19-mN1c-tTAA has the highest signal-to-noise ratio.</p>
+
                        <p>For more details, please check <a href="/Team:Fudan-TSI/Part_Collection">our parts collection page</a>.
+
                        </p>
+
                    </div>
+
                </main>
+
            </div>
+
  
            <!--Abstract on content page-->
+
  <p class="flow-text">For more information of other composite parts, please refer to <a href="/Team:Fudan-TSI/Part_Collection">the part collection page</a> and <a target="_blank" href="http://parts.igem.org/">the iGEM Part Registry</a> ranging from BBa_K3257100 to BBa_K3257118.</p>
            <div id="abstractContent" class="z-depth-2">
+
                <a href="#!"><img alt=alt="project summary" src="https://static.igem.org/mediawiki/2018/9/96/T--Fudan--X.svg"></a>
+
                <div class="container">
+
                    <h2 style="margin: 0;padding: 10px 0;">Project Summary</h2>
+
                    <p style="margin: 0">Contact-dependent signaling is critical for multicellular biological
+
                            events, yet customizing contact-dependent signal transduction between
+
                            cells remains challenging. Here we have developed the ENABLE toolbox, a
+
                            complete set of transmembrane binary logic gates. Each gate consists of
+
                            3 layers: Receptor, Amplifier, and Combiner. We first optimized synthetic
+
                            Notch receptors to enable cells to respond to different signals across the
+
                            membrane reliably. These signals, individually amplified intracellularly by
+
                            transcription, are further combined for computing. Our engineered zinc finger-based
+
                            transcription factors perform binary computation and output designed products.
+
                            In summary, we have combined spatially different signals in mammalian cells,
+
                            and revealed new potentials for biological oscillators, tissue engineering,
+
                            cancer treatments, bio-computing, etc. ENABLE is a toolbox for constructing
+
                            contact-dependent signaling networks in mammals. The 3-layer design principle
+
                            underlying ENABLE empowers any future development of transmembrane logic circuits,
+
                            thus contributes a foundational advance to Synthetic Biology.
+
                    </p>
+
                </div>
+
            </div>
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Latest revision as of 05:57, 16 November 2019

Composite Parts | 2019 iGEM Team:Fudan-TSI


Composite Parts

cover gif 1st added

For best composite part, we would like to present you with our Cre recombinase together with degradation tag. Cre recombinase (BBa_K3257044) is responsible for the recombination process between the reverse transcribed cDNA and the target Gene of Interest (GOI), which is rather one of the most important processes in our system.

Because of the leakage of uninduced Cre expression, we have spent much effort in lowering the steady-state expression level of Cre. An important approach is to attach 5 different types of degradation tags after the CDS of Cre. Using EGFP (BBa_E0040) as a reporter, we can see that the degradation rate of degradation tag with amino acid residual sequence of AANDENWVLAA (BBa_K3257073) is moderate for Cre recombinase to reach a steady but relatively low level of expression (Figure 1).

Figure 1. Degradation tag greatly reduces the protein level at stable state.
WT represents the positive control of EGFP without any tag attachment. The five degradation tags are represented by their last five amino acid sequence. The vertical axe shows the quantitative analysis of EGFP fluorescence (excitation wavelength: 485 nm; detection wavelength: 528 nm), normalized by cell amount (OD600). The fluorescence is quantified by the concentration of green fluorescein, cell number is quantified by the number of silicon beads, both are from the distributed measurement kit. Fluorescence below detection level are eliminated. Error bar stands for the SEM of 3 replicates. t-test is performed between WT and each degradation tag, P<0.0001 (****).

Transformed into BL21(DE3) with another plasmid containing lox sites and analyzed by colony PCR, we can see that DNA cleavage between identical-oriented loxP sites happens indicating the normal function of Cre recombinase (Figure 2). For more information of other composite parts, please refer to the part collection page and the iGEM Part Registry ranging from BBa_K3257100 to BBa_K3257118.

Figure 2. The verification of DNA cleavage between LoxP sites.
Plasmids containing the Cre gene were co-transformed with plasmids containing mCherry flanked by LoxP sites. A pair of sequencing primers were used to amplify the mCherry gene. PCR product would be around 1000 bp while fragments cleaved by Cre recombinase would be approximately 250 bp. The positive control group is the PCR product of plasmids containing the original mCherry gene. The negative control group is the PCR product of plasmids containing the Cre gene only.

Combining these two results, we show that this composite part is able to express Cre recombinase which functions well in an E. coli cell at a relatively low expression level, which is we need for new recombinants accumulating during the R-Evolution process.

In the future, iGEMers and synthetic biologists may use this part for homologous recombination with different degradation tags and promoters based on their own requirements.

For more information of other composite parts, please refer to the part collection page and the iGEM Part Registry ranging from BBa_K3257100 to BBa_K3257118.