Difference between revisions of "Team:Fudan-TSI/Notebook"

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{{Fudan-TSI}}<script src="https://code.jquery.com/jquery-1.11.3.min.js"></script>
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{{Fudan-TSI}}<!-- jquery loaded by HQ 1.12.4 -->
−
<html lang="en">
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<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.
+
  <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.
+
  <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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-->
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<style>
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<!-- LC check on 2018-10-18 -->
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/*****************************************************************************/
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<head>
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/* DEFAULT WIKI SETTINGS */
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    <meta charset="UTF-8">
+
/*****************************************************************************/
 +
  #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>Notebook | 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 rel="stylesheet" href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/Fudan-font-awesome.css&action=raw&ctype=text/css" />
+
    <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">Notebook</span></p>
 +
     </div></li>
 +
    <li>
 +
      <ul class="collapsible expandable">
 +
        <li class="onThisPageNav"><span>On this page</span></li>
 +
        <li class="onThisPageNav"><a href="#section1">section1</a></li>
 +
        <li class="onThisPageNav"><a href="#section2">section2</a></li>
 +
        <li class="onThisPageNav"><a href="#section3">section3</a></li>
 +
        <li class="onThisPageNav"><a href="#section4">section4</a></li>
  
−
    <!-- Materialize 1.0.0-rc.2 (Material Design like) -->
+
        <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 active"><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"><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>
−
    <link rel="stylesheet" href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/materialize.css&action=raw&ctype=text/css">
+
      </ul><!-- .expandable -->
 +
    </li>
 +
    <li><div class="placeHolder"></div></li>
 +
  </ul>
 +
  </header>
  
−
    <!-- Clear default CSS settings; CSS reset -->
+
  <div id="pageContent">
−
    <style>
+
      <div id="contentBanner" class="figureBanner">
−
        *{margin: 0;padding: 0;list-style: none;}
+
          <div class="row">
−
         /* via: https://blog.csdn.net/weixin_41014370/article/details/79523637 */
+
              <div class="col s12 hide-on-med-and-up">
−
 
+
                  <h1><br/>Notebook</h1>
−
         /** 清除内外边距 **/
+
                  <p class="flow-text">We hereby present a toolbox for <i>in vivo</i> continuous mutation library construction. Our toolbox is orthogonal and provides a wide range of applications among various species.</p>
−
         body, h1, h3, h3, h4, h5, h6, hr, p, blockquote, /* structural elements 结构元素 */
+
              </div>
−
         dl, dt, dd, ul, ol, li, /* list elements 列表元素 */
+
          </div>
−
         pre, /* text formatting elements 文本格式元素 */
+
          <div class="hide-on-small-only">
−
         form, fieldset, legend, button, input, textarea, /* form elements 表单元素 */
+
<style>
−
        th, td /* table elements 表格元素 */ {
+
#demo {width:100%;height:100%;position:relative;z-index:-100;}
−
            margin: 0;
+
#demo svg {width:100%;height:100%;position:fixed;}
−
            padding: 0;
+
#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");
 +
          }
 
         }
 
         }
  
−
        /** 设置默认字体 **/
 
  
−
         /* @@@@ h1, h3, h3, h4, h5, h6 { font-size: 100%; }*/
+
         // calc circumcircle center x/y, radius
−
         address, cite, dfn, em, var { font-style: normal; } /* 将斜体扶正 */
+
        m1  = -((xJ - xI) / (yJ - yI));
−
         code, kbd, pre, samp { font-family: courier new, courier, monospace; } /* 统一等宽字体 */
+
        m2  = -((xK - xJ) / (yK - yJ));
−
         /* @@@@ small { font-size: 12px; } /* 小于 12px 的中文很难阅读，让 small 正常化 */
+
        xMidIJ = (xI + xJ) / 2.0;
 +
        xMidJK = (xJ + xK) / 2.0;
 +
        yMidIJ = (yI + yJ) / 2.0;
 +
        yMidJK = (yJ + yK) / 2.0;
 +
        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;
 +
            }
 +
          }
  
−
        /** 重置列表元素 **/
 
−
        ul, ol { list-style: none; }
 
  
−
        /** 重置文本格式元素 **/
+
          // point outside circumcirc = leave candidates
−
        a { text-decoration: none; }
+
          dy = vertices[c][1] - candidates[j].y;
−
         a:hover { text-decoration: underline; }
+
          if(dx * dx + dy * dy - candidates[j].r > EPSILON)
 +
            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);
 +
              }
 +
            }
 +
          }
  
  
−
         /** 重置表单元素 **/
+
         // done
−
         legend { color: #000; } /* for ie6 */
+
         return candidates;
−
         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 */
+
      })();
−
         /* 注：optgroup 无法扶正 */
+
      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);
 +
              }
 +
            }
 +
          }
  
−
        /** 重置表格元素 **/
+
          var g = createRandomTesselation();
−
         table { border-collapse: collapse; border-spacing: 0; }
+
          n = g.children.length;
−
     </style>
+
          for (i = n; i--; ) {
−
    <title>2019 Team:Fudan-TSI Notebook</title>
+
          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});
−
</head>
+
          }
 +
          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 notebook" src="https://static.igem.org/mediawiki/2019/4/4b/T--Fudan-TSI--coverNotebook.gif" /></center></div>
 +
          </div>
 +
      </div>
  
−
<body>
+
<!--////////////////////////////////////////////////////
−
<!-- Fudan div at igem.org -->
+
      do not edit above, if must BE CAREFUL
−
<div id="FudanWrapper" class="white">
+
  //////////////////////////////////////////////////////-->
−
    <div id="FudanBody" class="white">
+
      <div class="container">
−
        <header>
+
          <!-- side navigator of page content -->
−
            <!-- empty bar -->
+
          <!-- main content of the page -->
−
            <div id="emptyBar" style="position:relative;width: 100%;"></div>
+
          <main style="margin:0"><article>
−
 
+
−
            <!-- Navigation bar 2019-9-15 -->
+
−
            <nav id="topNav" class="white 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/2019/3/3c/T--Fudan-TSI--Logo0.gif"></a>
+
−
                    </div>
+
−
                    <ul id="nav-mobile" class="right">
+
−
                        <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 -->
+
−
            <!-- Slide-out navigator contents 2019-9-15 -->
+
−
            <ul id="slide-out" class="sidenav">
+
−
                <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">Notebook</span></p>
+
−
                </div></li>
+
−
                <li>
+
−
                    <ul class="collapsible expandable">
+
−
                        <li class="onThisPageNav"><span>Team: Fudan-TSI</span></li>
+
−
<li><div class="collapsible-header"><span>Project</span></div>
+
−
    <div class="collapsible-body"><ul>
+
−
        <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/Applied_Design">Applied Design</a></li>
+
−
        <li><a href="/Team:Fudan-TSI/Experiments">Experiments</a></li>
+
−
        <li><a href="/Team:Fudan-TSI/Judging">Judging</a></li>
+
−
    </ul></div>
+
−
</li>
+
−
<li><div class="collapsible-header"><span>Results</span></div>
+
−
    <div class="collapsible-body"><ul>
+
−
        <li><a href="/Team:Fudan-TSI/Results#ReverseTranscription">Reverse Transcription</a></li>
+
−
        <li><a href="/Team:Fudan-TSI/Results#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></div>
+
−
</li>
+
−
<li><div class="collapsible-header"><span>Model</span></div>
+
−
    <div class="collapsible-body"><ul>
+
−
        <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></div>
+
−
</li>
+
−
<li><div class="collapsible-header"><span>Parts</span></div>
+
−
    <div class="collapsible-body"><ul>
+
−
        <li><a href="/Team:Fudan-TSI/Basic_Part">Basic parts</a></li>
+
−
        <li><a href="/Team:Fudan-TSI/Composite_Part">Composite parts</a></li>
+
−
        <li><a href="/Team:Fudan-TSI/Improve">Improved parts</a></li>
+
−
        <li><a href="/Team:Fudan-TSI/Part_Collection">Part collection</a></li>
+
−
    </ul></div>
+
−
</li>
+
−
<li><div class="collapsible-header"><span>Outreach</span></div>
+
−
    <div class="collapsible-body"><ul>
+
−
        <li><a href="/Team:Fudan-TSI/Public_Engagement">Education &amp; Public engagement</a></li>
+
−
        <li><a href="/Team:Fudan-TSI/Integrated_Human_Practice">Integrated human practice</a></li>
+
−
        <li><a href="/Team:Fudan-TSI/Collaborations">Collaborations</a></li>
+
−
        <li><a href="/Team:Fudan-TSI/Safety">Safety</a></li>
+
−
    </ul></div>
+
−
</li>
+
−
<li><div class="collapsible-header"><span>Team</span></div>
+
−
    <div class="collapsible-body"><ul>
+
−
        <li><a href="/Team:Fudan-TSI/Team">Members</a></li>
+
−
        <li><a href="/Team:Fudan-TSI/Attributions">Attributions</a></li>
+
−
        <li><a href="https://2018.igem.org/Team:Fudan/Heritage" target=_blank>Heritage</a></li>
+
−
    </ul></div>
+
−
</li>
+
−
                    </ul><!-- .expandable -->
+
−
                </li>
+
−
                <li><div class="placeHolder"></div></li>
+
−
            </ul>
+
−
        </header>
+
−
 
+
−
        <div id="pageContent" style="">
+
−
            <div id="contentBanner" class="figureBanner">
+
−
                <div class="row">
+
−
                    <div class="col s12 m6 valign-wrapper hide-on-med-and-up">
+
−
                        <h1>Our notebook</h1>
+
−
                    </div>
+
−
                    <div class="col s12 m6 valign-wrapper hide-on-med-and-up">
+
−
                        <span>Here we present a main outline of our progress throughout the year.</span>
+
−
                    </div>
+
−
                </div>
+
−
                <div id="figureBannerTitle" class="hide-on-small-only">
+
−
                    <h1>Our notebook</h1>
+
−
                    <p class="flow-text"><span>Here we present a main outline of our progress throughout the year.</span></p>
+
−
                </div>
+
−
                <div class="hide-on-small-only">
+
−
                    <img src="https://static.igem.org/mediawiki/2018/b/ba/T--Fudan--title_notebook.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 -->
+
<div class="section container">
−
            <div class="container">
+
  <embed src="https://static.igem.org/mediawiki/2019/a/a3/T--Fudan-TSI--Notebook.pdf" width="100%" height="600px" type="application/pdf" />
−
                <!-- side navigator of page content -->
+
  <p>Here is <a target="_blank" href="https://static.igem.org/mediawiki/2019/a/a3/T--Fudan-TSI--Notebook.pdf">the link</a> to download the file above.</p>
−
                <main style="margin:0">
+
−
                    <div class="section container">
+
−
                        <h2>Monthly Highlights</h2>
+
−
<h3>April</h3>
+
−
<ul>
+
−
<li>First functional SynNotch constructed
+
−
</li><li>Developed a simple testification method of SynNotch—shaking beads linked with antigen
+
−
</li><li>Transcription factor and promotor pairs constructed and tested</li>
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                    <p class="flow-text" style="margin:0">Mutation library generation is critical for biological and medical research, but current methods cannot mutate a specific sequence continuously without manual intervention. Here we present a toolbox for <i>in vivo</i> continuous mutation library construction. First, the target DNA is transcribed into RNA. Next, our reverse transcriptase reverts RNA into cDNA, during which the target is randomly mutated by enhanced error-prone reverse transcription. Finally, the mutated version replaces the original sequence through recombination. These steps will be carried out iteratively, generating a random mutation library of the target with high efficiency as mutations accumulate along with bacterial growth. Our toolbox is orthogonal and provides a wide range of applications among various species. R-Evolution could mutate coding sequences and regulatory sequences, which enables the <i>in vivo</i> evolution of individual proteins or multiple targets at a time, promotes high-throughput research, and serves as a foundational advance to synthetic biology.
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Latest revision as of 05:51, 16 November 2019

Notebook | 2019 iGEM Team:Fudan-TSI


Notebook

We hereby present a toolbox for in vivo continuous mutation library construction. Our toolbox is orthogonal and provides a wide range of applications among various species.

cover notebook

Here is the link to download the file above.