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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"> |
| − | <!-- | + | <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" /><!-- /https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/Fudan-css.css&action=raw&ctype=text/css --> |
| − | --> | + | <style> |
| − | <!-- LC check on 2018-10-26 --> | + | /*****************************************************************************/ |
| − | <head> | + | /* DEFAULT WIKI SETTINGS */ |
| − | <meta charset="UTF-8">
| + | /*****************************************************************************/ |
| | + | #home_logo, #sideMenu { display:none; } |
| | + | #sideMenu, #top_title, .patrollink { display:none; } |
| | + | #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>Part Improvement | 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"> |
| | | | |
| − | <!-- CSS --> | + | <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 practices</a></li><li class="hide-on-med-and-down"><a class="dropdown-trigger" data-target="dropdown6">Team</a></li> |
| − | <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" /> | + | <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 design</a></li> |
| | + | </ul> |
| | + | <ul id="dropdown2" class="dropdown-content"> |
| | + | <li><a href="/Team:Fudan-TSI/Demonstrate#ReverseTranscription">Reverse 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 parts</a></li> |
| | + | <li><a href="/Team:Fudan-TSI/Composite_Part">Composite parts</a></li> |
| | + | <li><a href="/Team:Fudan-TSI/Improve">Part improvement</a></li> |
| | + | <li><a href="/Team:Fudan-TSI/Part_Collection">Part collection</a></li> |
| | + | </ul> |
| | + | <ul id="dropdown5" class="dropdown-content"> |
| | + | <li><a href="/Team:Fudan-TSI/Public_Engagement">Public engagement</a></li> |
| | + | <li><a href="/Team:Fudan-TSI/Human_Practices#IntegratedHumanPractice">Integrated 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> |
| | | | |
| − | <!-- Font-awesome icons 4.7.0 -->
| |
| − | <link href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/Fudan-font-awesome.css&action=raw&ctype=text/css" rel="stylesheet" />
| |
| | | | |
| − | <!-- Materialize 1.0.0-rc.2 (Material Design like) -->
| + | <ul id="slide-out" class="sidenav"> |
| − | <link rel="stylesheet" href="https://2019.igem.org/wiki/index.php?title=Template:Fudan-TSI/materialize.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">Part Improvement</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> |
| | | | |
| − | <!-- 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/>Part Improvement</h1> |
| − | /** 清除内外边距 **/ | + | </div> |
| − | 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 class="hide-on-small-only"> |
| − | pre, /* text formatting elements 文本格式元素 */ | + | <style> |
| − | form, fieldset, legend, button, input, textarea, /* form elements 表单元素 */ | + | #demo {width:100%;height:100%;position:relative;z-index:-100;} |
| − | th, td /* table elements 表格元素 */ {
| + | #demo svg {width:100%;height:100%;position:fixed;} |
| − | margin: 0;
| + | #demo svg g {mix-blend-mode:lighten;} |
| − | padding: 0;
| + | #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 -Improve</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 gif 1st added" src="https://static.igem.org/mediawiki/2019/2/23/T--Fudan-TSI--coverImprovedParts.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 -->
| + | <ul id="pageContentNav" class="hide-on-med-and-down z-depth-0"> |
| − | <div id="emptyBar" style="position:relative;width: 100%;"></div>
| + | <li class="onThisPageNav"><a href="#section1">Overview</a></li> |
| | + | <li class="onThisPageNav"><a href="#section2">Better orthogonality</a></li> |
| | + | <li class="onThisPageNav"><a href="#section3">Stronger operon</a></li> |
| | + | <li class="onThisPageNav"><a href="#section4">Less leakage</a></li> |
| | + | </ul> |
| | + | <!-- main content of the page --> |
| | + | <main><article> |
| | | | |
| − | <!-- Navigation bar -->
| + | <div id="section1" class="section container scrolSpy"> |
| − | <!-- Dropdown and List elements in navigation bar -->
| + | <p class="flow-text">We have upgraded LacI gene <a target="_blank" href="http://parts.igem.org/Part:BBa_K3257012">(BBa_C0012)</a> to a better version <a target="_blank" herf="http://parts.igem.org/Part:BBa_K3257045">(BBa_K3257045)</a>.</p> |
| − | <!-- Slide-out navigator contents -->
| + | <p class="flow-text">LacI is one of the genes in Lac operon encoding the inhibitor protein binding to LacO <a target="_blank" href="http://parts.igem.org/Part:BBa_K3257066">(BBa_K3257066)</a> sites (cis-acting element). In response to IPTG, the inhibitor protein detaches from LacO and enables the transcription of downstream genes. We mutated some specific sites in the LacI gene to improve its sensibility to IPTG <a href="https://www.ncbi.nlm.nih.gov/pubmed/30478458" target="_blank">(Christopher Voigt, et al.)</a>. Using EGFP as a reporter, its fluorescence intensity demonstrates a lower level of leakage and the same level of expression before and after the induction of IPTG. Also, we induce the improved Lac operon by arabinose to verify its orthogonal response to IPTG.</p> |
| − | </header>
| + | <p class="flow-text">With LacIq promoter <a href="http://parts.igem.org/Part:BBa_K3257003" target="_blank">(BBa_K3257003)</a> and rrnB T1 terminator <a href="http://parts.igem.org/Part:BBa_K3257020" target="_blank">(BBa_K3257020)</a>, improved LacI protein can be expressed and function properly in the <i>Escherichia coli</i> BL21(DE3). We used EGFP as a reporter controlled by our improved Lac operon and measured its green fluorescence over time.</p> |
| | + | <p class="flow-text">We cut out BBa_C0012 between the 9<sup>th</sup> and 1153<sup>rd</sup> nucleotide, mutated the 60<sup>th</sup> nucleotide from C to A, the 61<sup>st</sup> nucleotide from A to T, 136<sup>th</sup> nucleotide from C to T, the 490<sup>th</sup> nucleotide from T to A, the 500<sup>th</sup> nucleotide from A to G and the 1001<sup>st</sup> nucleotide from C to G of it and added a stop codon at the end of it.</p> |
| | + | <p class="flow-text">According to our experiment, our Lac operon is improved in the following three main aspects.</p> |
| | + | </div> |
| | | | |
| − | <div id=" pageContent" style=""> | + | <div id="section2" class="section container scrolSpy"> |
| − | <div id="contentBanner" class="figureBanner">
| + | <h4>Lower response to arabinose, better orthogonality</h4> |
| − | <div class="row">
| + | <p class="flow-text">Crosstalk between the response to IPTG and arabinose has been a defect of the wild type Lac operon. When 4 mM arabinose is added, a few lac inhibitors would detach from lac operator. This means that it is induced in a relatively low but unignorable level. According to the measurement of our experiment, our improved LacI can respond to IPTG with better orthogonality. As shown in <a href="#Fig1">Figure 1</a>, when 4 mM arabinose is added, oLacI (wild-type LacI) is induced at a significantly higher level than iLacI (improved LacI).</p> |
| − | <div class="col s12 m6 valign-wrapper hide-on-med-and-up">
| + | |
| − | <h1>Parts improvement</h1>
| + | |
| − | </div>
| + | |
| − | <div class="col s12 m6 valign-wrapper hide-on-med-and-up">
| + | |
| − | <span>In an effort to innovate and improve, we enhanced our engineered transmembrane binary logic gates </span>
| + | |
| − | </div>
| + | |
| − | </div>
| + | |
| − | <div id="figureBannerTitle" class="hide-on-small-only">
| + | |
| − | <h1>Parts improvement</h1>
| + | |
| − | <p><span>In an effort to innovate and improve, we enhanced our engineered transmembrane binary logic gates </span></p>
| + | |
| − | </div>
| + | |
| − | <div class="hide-on-small-only">
| + | |
| − | <img src="https://static.igem.org/mediawiki/2018/7/72/T--Fudan--title_partsimprovement.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=" figureHolder" id=" Fig1"> |
| − | | + | <img class="responsive-img" src="https://static.igem.org/mediawiki/2019/d/d0/T--Fudan-TSI--Improved_Fig1.png" /> |
| − | <main>
| + | <p>< b> Figure 1. The expression level of EGFP controlled by different versions of LacI and inducers, or under different promoters.</ b>< br/> |
| − | <!-- side navigator of page content -->
| + | The origin point indicates the time when different inducers are added (1 mM IPTG and/or 4 mM Arabinose). The title of the graph shows which kind of inducer is added to the culture. The horizontal axe shows the duration of time, the vertical axe shows the quantified level of EGFP expression. The fluorescence level (excitation wavelength: 485 nm; detection wavelength: 528 nm) is quantified by the concentration of fluorescein, and normalized by the measured OD600 equivalent to the number of beads in the system. oLacI stands for the wildtype LacI, iLacI stands for our improved version of LacI. +LacO indicates that the promoter constitutes a LacO sequence. Control is the negative control plasmid which does not constitute an EGFP sequence. Error bar in the two graphs on the first row indicates the SEM of three replicates. The second row showed only the mean amount of three replicate.</p> |
| − | <ul id="pageContentNav" class="hide-on-med-and-down z-depth-0">
| + | </div> |
| − | <li><a href="/Team:Fudan-TSI/Basic_Part">Basic parts</a></li>
| + | </div> |
| − | <li><a href="/Team:Fudan-TSI/Composite_Part">Composite parts</a></li>
| + | |
| − | <li><a href="/Team:Fudan-TSI/Optimization">Optimization</a></li>
| + | |
| − | <li><a href="/Team:Fudan-TSI/Part_Collection">Part collection</a></li>
| + | |
| − | <li>Parts improvement</li>
| + | |
| − | <li class="onThisPageNav"><a href="#section1">Introduction</a></li>
| + | |
| − | <li class="onThisPageNav"><a href="#section2">Responsive elements</a></li>
| + | |
| − | <li class="onThisPageNav"><a href="#section3">pSV40 vs pCMV</a></li>
| + | |
| − | <li><a href="/Team:Fudan-TSI/Measurement">Quantification</a></li>
| + | |
| − | </ul>
| + | |
| − | <div id="section1" class="section container scrolSpy">
| + | |
| − | <h2>Introduction</h2>
| + | |
| − | <p> Last year our team has proposed a < a href="https://2017.igem.org/Team:Fudan/Part_Collection" target="_blank"> SynTF-SynPro approach</a> which enables others to construct a customized and orthogonal transcriptional network in mammalian cells. The structures of the corresponding silencing- or activating-form of SynPros were pSV40-N*RE and N*RE-minCMV, in which N*RE is short for responsive elements of N repeats. | + | |
| − | </p>
| + | |
| − | <p>
| + | |
| − | This year we took it a step further to create our engineered transmembrane binary logic gates in eukaryotic cells based on the foundational concepts we have constructed upon last year. We made use of the SynTF-SynPro system to function as our Combiner, which executes the final computation of our genetic circuits. To improve the signal-to-noise ratio of our Combiner and to allow others to more easily use our toolbox, we attempted to optimize the structure of the SynPros and constructed N*RE-CMV, which replaces the pSV40-N*RE to respond to transcriptional repressors. Furthermore, we also conducted experiments to characterize our N*RE-CMV, ensuring that it performs exceedingly better than the previous pSV40-N*RE. We have substituted all the pSV40-N*RE with N*RE-CMV when wiring our genetic circuits and picked 8*ZF21.16-CMV for specific demonstration of our parts improvement. For more details, refer to the <a href="http://parts.igem.org/Part:BBa_K2446030" target="_blank">existing BioBrick page</a> or the <a href="http://parts.igem.org/Part:BBa_K2549029" target="_blank">improved BioBrick page</a>.
| + | |
| − | </p>
| + | |
| − | </div>
| + | |
| − | <div id="section2" class="section container scrolSpy">
| + | |
| − | <h2>Place of responsive elements</h2>
| + | |
| − | <p>We have experimentally discovered that the place of N*RE can have an impact on basal expression of SynPros. Thus, when designing transcription repressing circuit, we hope that the addition of the N*RE will not bother the original expression of the promotor. Unfortunately, we realized that when the N*RE is placed downstream the promotor, the basal expression of the promotor is effected without the transcriptional repressor. Therefore, we made an attempt to adjust the position of N*RE to upstream of the promotor. Interestingly, the basal expression of the promotor is less affected as compared to the previous design. Actually, similar phenomenon have been reported previously that reporter activity was highly variable among the four different TALE binding sites introduced between the promoter and the reporter coding sequence while the introduction of multiple copies of each of the four different operators upstream from the promoter caused only minimal variability in reporter expression
| + | |
| − | as suggested by <a href="http://dx.doi.org/10.1038/nchembio.1433" target=_blank>Gaber R, et al, 2014 (PMID: 24413461)</a>.
| + | |
| − | </p>
| + | |
| − | </div>
| + | |
| − | <div id="section3" class="section container scrolSpy">
| + | |
| − | <h2>pSV40 vs pCMV
| + | |
| − | </h2>
| + | |
| − | <p>To better verify that the transcription repressor can effectively repress the expression of its responsive circuit, we attempted to increase the basal expression for a more precise comparison. As a result, we designed a simple genetic circuit in which a EGFP-P2A was put downstream the promotor to test and compare the basal expression of pSV40 and pCMV. We used fluorescence microscopy to detect the expression of the reporter gene 24 hours after transient transfecting 293T cells with the two mentioned circuits, respectively. We found that pCMV has a significantly higher basal expression than that of pSV40, providing us a more ideal alternation to construct our transcriptional repressor-based Combiner circuit.
| + | |
| − | </p>
| + | |
| − | <div class="figureHolder width40" style="margin: 23px auto 0 auto;">
| + | |
| − | <img class="responsive-img" src="https://static.igem.org/mediawiki/2018/c/c2/T--Fudan--improve-1.png">
| + | |
| − | </div>
| + | |
| − | <p style="margin-top:0;text-indent: 0;"><b>Figure 1. Flow cytometry data of previously designed SynPros based on pSV40.</b> It can be clearly identified that the basal expression of pSV40 is easily effected by the adding of responsive elements. (sTF is short for silencing-form transcriptional factors.)
| + | |
| − | </p>
| + | |
| − | <div class="figureHolder width40" style="margin: 23px auto 0 auto;"> | + | |
| − | <img class="responsive-img" src="https://static.igem.org/mediawiki/2018/b/bb/T--Fudan--improve-2.png">
| + | |
| − | </div>
| + | |
| − | <p style="margin-top:0;text-indent: 0;"><b>Figure 2. Flow cytometry data of the improved design of SynPros based on pCMV.</b> It is shown that the basal expression of pCMV is barely effected by the adding of responsive elements. (sTF is short for silencing-form transcriptional factors.)
| + | |
| | | | |
| − | </p>
| + | <div id="section3" class="section container scrolSpy"> |
| − | <div class=" figureHolder width45" style=" margin: 23px auto 0 auto;"> | + | <h4>Higher induction level than the wild-type Lac operon when induced by IPTG</h4> |
| − | <img class="responsive-img" src="https://static.igem.org/mediawiki/2018/0/06/T--Fudan--improve-3.png">
| + | <p class=" flow-text"> Our improved Lac operon does not malfunction and can be normally induced by IPTG. When 1 mM IPTG is added, EGFP controlled by both operons can be induced and expressed at relatively the same level <a href="#Fig1">(Figure 1)</ a> , while the level of induction under the control of iLacI is significantly higher than that of oLacI < a href="#Fig2"> (Figure 2)</ a> .</ p> |
| − | </div>
| + | <div class=" figureHolder" id=" Fig2"> |
| − | <p style=" margin- top:0;text -indent: 0;"> <b>Figure 3. Fluorescence intensity comparison of pCMV-EGFP -P2A and pSV40-EGFP-P2A 24 hours after transfection.</ b> The expression level of pCMV is significantly higher than pSV40. | + | <img class="responsive-img" src="https://static.igem.org/mediawiki/2019/d/d6/T--Fudan-TSI--Improved_Fig2.png" /> |
| − | | + | <p><b>Figure 2. The induction level of EGFP under different repressor and promoters.</b><br/> |
| − | </p>
| + | Induction level is calculated by dividing fluorescence level after 9 h of induction by 1 h afterwards. The fluorescence level is quantified as in <a href="#Fig1">Figure 1</a>. oLacI stands for the wildtype LacI, iLacI stands for our improved version of LacI. +LacO indicates that the promoter constitutes a LacO sequence. t test analysis shows that the induction level of iLacI is significantly higher than oLacI, *** indicates that p=0.0002.</p> |
| − | </div>
| + | </div> |
| − | </main>
| + | </div> |
| − | </div>
| + | |
| − | | + | |
| − | <!--Abstract on content page-->
| + | |
| − | <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>
| + | |
| | | | |
| − | <!-- Floating Btns -->
| + | <div id="section4" class="section container scrolSpy"> |
| − | <div class="floatingBtn"> | + | <h4>Lower uninduced leakage</h4> |
| − | <a href="#!" id="abstractBtn" class="btn">
| + | <div class=" figureHolder" id=" Fig3"> |
| − | <i class="fa fa-sticky-note" style="font-size: 30px;line-height: 50px"></i>
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| − | </a>
| + | <p><b>Figure 3. The basal fluorescence level of EGFP controlled by different repressors.</b><br/> |
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| + | The bar indicates the mean fluorescence level during the 10 h with no inducer in the culture. The fluorescence level is quantified as in <a href=" #Fig3"> Figure 1</a>. oLacI stands for the wildtype LacI, iLacI stands for our improved version of LacI. Control is below the detection level and not shown. Error bar indicates the SEM of fluorescence signal in the 10 h. Paired t test analysis shows that iLacI has a significantly lower of fluorescence than oLacI, p=0. 0057 (**) .</ p> |
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| + | < p class=" flow- text"> The uninduced leakage level is also an important parameter of an operon. Improved LacI lowers the leakage level compared to the wild- type one. The figure below <a href=" #Fig3"> (Figure 3)</a> is the measurement of the fluorescence of EGFP controlled by wild- type and improved Lac operon. When no IPTG or arabinose is added, the fluorescence of EGFP controlled by improved Lac operon much lower than the fluorescence of EGFP controlled by wild- type Lac operon <a href=" #Fig1"> )Figure 1</a><a href=" #Fig3"> & 3)</a>.</ p> |
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