Team:SUSTC-Shenzhen-B/lab introduction

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<html>
<html>
<head>
<head>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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  <meta charset="utf-8" />
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<title>SUSTC iGEM Theme - Free CSS Template</title>
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  <meta name="description" content="" />
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<meta name="keywords" content="beauty class, free theme, website design, bokehs, pink, orange, templatemo, CSS, HTML" />
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  <meta name="author" content="tengattack" />
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<meta name="description" content="Beauty Class Theme, pinky background gradient with bokehs, free CSS template provided by templatemo.com" />
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  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<link href="http://www.templatemo.com/templates/templatemo_353_beauty_class/css/templatemo_style.css" rel="stylesheet" type="text/css" />
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  <title>Title</title>
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<link rel="stylesheet" href="http://www.templatemo.com/templates/templatemo_353_beauty_class/css/nivo-slider.css" type="text/css" media="screen" />
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<style type="text/css">
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<link rel="stylesheet" type="text/css" href="http://www.templatemo.com/templates/templatemo_353_beauty_class/css/ddsmoothmenu.css" />
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#globalWrapper {width: 100%;  }
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#top-section {width: 100%; height:100%; border:none;}
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#p-logo {display:none;}
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#search-controls {display:none;}
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.printfooter {display:none;}
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#footer-box {border:none;}
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.firstHeading {display:none;}
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#content { border:none !important; width:1024px !important; background: url('') !important;}
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#bodyContent {border:none;  }
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#catlinks {display:none; }
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#footer-box {display:none; }
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#menubar {display:none; }
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<script language="javascript" type="text/javascript">
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/* googleapis-font */
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function clearText(field)
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@font-face {
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{
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@font-face {
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}
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@font-face {
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  src: local('Open Sans'), local('OpenSans'), url(http://themes.googleusercontent.com/static/fonts/opensans/v6/cJZKeOuBrn4kERxqtaUH3T8E0i7KZn-EPnyo3HZu7kw.woff) format('woff');
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.pp_middle{background:url(../images/facebook/contentPatternBottom.png) top left repeat-x}div.facebook .pp_bottom .pp_right{background:url(../images/facebook/sprite.png) -110px -80px no-repeat}div.pp_pic_holder a:focus{outline:0}div.pp_overlay{background:#000;display:none;left:0;position:absolute;top:0;width:100%;z-index:9500}div.pp_pic_holder{display:none;position:absolute;width:100px;z-index:10000}.pp_content{height:40px;min-width:40px}* html .pp_content{width:40px}.pp_content_container{position:relative;text-align:left;width:100%}.pp_content_container .pp_left{padding-left:20px}.pp_content_container .pp_right{padding-right:20px}.pp_content_container .pp_details{float:left;margin:10px 0 2px}.pp_description{display:none;margin:0}.pp_social{float:left;margin:0}.pp_social .facebook{float:left;margin-left:5px;overflow:hidden;width:55px}.pp_social .twitter{float:left}.pp_nav{clear:right;float:left;margin:3px 10px 0 0}.pp_nav p{float:left;margin:2px 4px;white-space:nowrap}.pp_nav .pp_play,.pp_nav .pp_pause{float:left;margin-right:4px;text-indent:-10000px}a.pp_arrow_previous,a.pp_arrow_next{display:block;float:left;height:15px;margin-top:3px;overflow:hidden;text-indent:-10000px;width:14px}.pp_hoverContainer{position:absolute;top:0;width:100%;z-index:2000}.pp_gallery{display:none;left:50%;margin-top:-50px;position:absolute;z-index:10000}.pp_gallery div{float:left;overflow:hidden;position:relative}.pp_gallery ul{float:left;height:35px;margin:0 0 0 5px;padding:0;position:relative;white-space:nowrap}.pp_gallery ul a{border:1px rgba(0,0,0,.5) solid;display:block;float:left;height:33px;overflow:hidden}.pp_gallery ul a img{border:0}.pp_gallery li{display:block;float:left;margin:0 5px 0 0;padding:0}.pp_gallery li.default a{background:url(../images/facebook/default_thumbnail.gif) 0 0 no-repeat;display:block;height:33px;width:50px}.pp_gallery .pp_arrow_previous,.pp_gallery .pp_arrow_next{margin-top:7px!important}a.pp_next{background:url(../images/light_rounded/btnNext.png) 10000px 10000px no-repeat;display:block;float:right;height:100%;text-indent:-10000px;width:49%}a.pp_previous{background:url(../images/light_rounded/btnNext.png) 10000px 10000px no-repeat;display:block;float:left;height:100%;text-indent:-10000px;width:49%}a.pp_expand,a.pp_contract{cursor:pointer;display:none;height:20px;position:absolute;right:30px;text-indent:-10000px;top:10px;width:20px;z-index:20000}a.pp_close{display:block;line-height:22px;position:absolute;right:0;text-indent:-10000px;top:0}.pp_loaderIcon{display:block;height:24px;left:50%;margin:-12px 0 0 -12px;position:absolute;top:50%;width:24px}#pp_full_res{line-height:1!important}#pp_full_res .pp_inline{text-align:left}#pp_full_res .pp_inline p{margin:0 0 15px}div.ppt{color:#fff;display:none;font-size:17px;margin:0 0 5px 15px;z-index:9999}div.pp_default .pp_content,div.light_rounded .pp_content{background-color:#fff}div.pp_default #pp_full_res .pp_inline,div.light_rounded .pp_content .ppt,div.light_rounded #pp_full_res .pp_inline,div.light_square .pp_content .ppt,div.light_square #pp_full_res .pp_inline,div.facebook .pp_content .ppt,div.facebook #pp_full_res .pp_inline{color:#000}div.pp_default .pp_gallery ul li a:hover,div.pp_default .pp_gallery ul li.selected a,.pp_gallery ul a:hover,.pp_gallery li.selected a{border-color:#fff}div.pp_default .pp_details,div.light_rounded .pp_details,div.dark_rounded .pp_details,div.dark_square .pp_details,div.light_square .pp_details,div.facebook .pp_details{position:relative}div.light_rounded .pp_top .pp_middle,div.light_rounded .pp_content_container .pp_left,div.light_rounded .pp_content_container .pp_right,div.light_rounded .pp_bottom .pp_middle,div.light_square .pp_left,div.light_square .pp_middle,div.light_square .pp_right,div.light_square .pp_content,div.facebook .pp_content{background:#fff}div.light_rounded .pp_description,div.light_square .pp_description{margin-right:85px}div.light_rounded .pp_gallery a.pp_arrow_previous,div.light_rounded .pp_gallery a.pp_arrow_next,div.dark_rounded .pp_gallery a.pp_arrow_previous,div.dark_rounded .pp_gallery a.pp_arrow_next,div.dark_square .pp_gallery a.pp_arrow_previous,div.dark_square .pp_gallery a.pp_arrow_next,div.light_square .pp_gallery a.pp_arrow_previous,div.light_square .pp_gallery a.pp_arrow_next{margin-top:12px!important}div.light_rounded .pp_arrow_previous.disabled,div.dark_rounded .pp_arrow_previous.disabled,div.dark_square .pp_arrow_previous.disabled,div.light_square .pp_arrow_previous.disabled{background-position:0 -87px;cursor:default}div.light_rounded .pp_arrow_next.disabled,div.dark_rounded .pp_arrow_next.disabled,div.dark_square .pp_arrow_next.disabled,div.light_square .pp_arrow_next.disabled{background-position:-22px -87px;cursor:default}div.light_rounded .pp_loaderIcon,div.light_square .pp_loaderIcon{background:url(../images/light_rounded/loader.gif) center center no-repeat}div.dark_rounded .pp_top .pp_middle,div.dark_rounded .pp_content,div.dark_rounded .pp_bottom .pp_middle{background:url(../images/dark_rounded/contentPattern.png) top left repeat}div.dark_rounded .currentTextHolder,div.dark_square .currentTextHolder{color:#c4c4c4}div.dark_rounded #pp_full_res .pp_inline,div.dark_square #pp_full_res .pp_inline{color:#fff}.pp_top,.pp_bottom{height:20px;position:relative}* html .pp_top,* html .pp_bottom{padding:0 20px}.pp_top .pp_left,.pp_bottom .pp_left{height:20px;left:0;position:absolute;width:20px}.pp_top .pp_middle,.pp_bottom .pp_middle{height:20px;left:20px;position:absolute;right:20px}* html .pp_top .pp_middle,* html .pp_bottom .pp_middle{left:0;position:static}.pp_top .pp_right,.pp_bottom .pp_right{height:20px;left:auto;position:absolute;right:0;top:0;width:20px}.pp_fade,.pp_gallery li.default a img{display:none}
 +
</style>
<script type="text/javascript">
<script type="text/javascript">
-
ddsmoothmenu.init({
+
/*
-
mainmenuid: "templatemo_menu", //menu DIV id
+
* Superfish v1.4.8 - jQuery menu widget
-
orientation: 'h', //Horizontal or vertical menu: Set to "h" or "v"
+
* Copyright (c) 2008 Joel Birch
-
classname: 'ddsmoothmenu', //class added to menu's outer DIV
+
*
-
//customtheme: ["#1c5a80", "#18374a"],
+
* Dual licensed under the MIT and GPL licenses:
-
contentsource: "markup" //"markup" or ["container_id", "path_to_menu_file"]
+
*  http://www.opensource.org/licenses/mit-license.php
-
})
+
*  http://www.gnu.org/licenses/gpl.html
 +
*
 +
* CHANGELOG: http://users.tpg.com.au/j_birch/plugins/superfish/changelog.txt
 +
*/
-
</script>
+
;(function($){
 +
  $.fn.superfish = function(op){
-
<script type="text/javascript" src="http://www.templatemo.com/templates/templatemo_353_beauty_class/js/jquery-1-4-2.min.js"></script>
+
    var sf = $.fn.superfish,
-
<link rel="stylesheet" href="http://www.templatemo.com/templates/templatemo_353_beauty_class/css/slimbox2.css" type="text/css" media="screen" />
+
      c = sf.c,
-
<script type="text/JavaScript" src="http://www.templatemo.com/templates/templatemo_353_beauty_class/js/slimbox2.js"></script>
+
      $arrow = $(['<span class="',c.arrowClass,'"> &#187;</span>'].join('')),
-
</style>
+
      over = function(){
 +
        var $$ = $(this), menu = getMenu($$);
 +
        clearTimeout(menu.sfTimer);
 +
        $$.showSuperfishUl().siblings().hideSuperfishUl();
 +
      },
 +
      out = function(){
 +
        var $$ = $(this), menu = getMenu($$), o = sf.op;
 +
        clearTimeout(menu.sfTimer);
 +
        menu.sfTimer=setTimeout(function(){
 +
          o.retainPath=($.inArray($$[0],o.$path)>-1);
 +
          $$.hideSuperfishUl();
 +
          //if (o.$path.length &amp;&amp; $$.parents(['li.',o.hoverClass].join('')).length<1){over.call(o.$path);}
 +
          if (o.$path.length) {
 +
            if ($$.parents(['li.',o.hoverClass].join('')).length<1){over.call(o.$path);}
 +
          }
 +
        },o.delay);
 +
      },
 +
      getMenu = function($menu){
 +
        var menu = $menu.parents(['ul.',c.menuClass,':first'].join(''))[0];
 +
        sf.op = sf.o[menu.serial];
 +
        return menu;
 +
      },
 +
      addArrow = function($a){ $a.addClass(c.anchorClass).append($arrow.clone()); };
 +
     
 +
    return this.each(function() {
 +
      var s = this.serial = sf.o.length;
 +
      var o = $.extend({},sf.defaults,op);
 +
      o.$path = $('li.'+o.pathClass,this).slice(0,o.pathLevels).each(function(){
 +
        $(this).addClass([o.hoverClass,c.bcClass].join(' '))
 +
          .filter('li:has(ul)').removeClass(o.pathClass);
 +
      });
 +
      sf.o[s] = sf.op = o;
 +
      var bcheck = false;
 +
      if ($.fn.hoverIntent) {
 +
        if (!o.disableHI) bcheck = true;
 +
      }
-
<style type="text/css">
+
      $('li:has(ul)',this)[(bcheck) ? 'hoverIntent' : 'hover'](over,out).each(function() {
-
<!--我们需要先把igem原网站的一些东西删掉-->
+
        if (o.autoArrows) addArrow( $('>a:first-child',this) );
-
#globalWrapper
+
      })
-
{    width: 100%;
+
      .not('.'+c.bcClass)
-
}
+
        .hideSuperfishUl();
-
#top-section {width: 100%; height:100%; border:none;}
+
     
-
#p-logo {display:none;}
+
      var $a = $('a',this);
-
#search-controls {display:none;}
+
      $a.each(function(i){
-
.printfooter {display:none;}
+
        var $li = $a.eq(i).parents('li');
-
#footer-box {border:none;}
+
        $a.eq(i).focus(function(){over.call($li);}).blur(function(){out.call($li);});
-
.firstHeading {display:none;}
+
      });
-
#content
+
      o.onInit.call(this);
-
{      
+
     
-
        background-image: url(http://2012.igem.org/wiki/images/8/81/Sustc_shenzhen_b_Templatemo_main_bg.jpg);
+
     }).each(function() {
-
        background-position: top center;
+
      var menuClasses = [c.menuClass];
-
background-repeat: no-repeat;
+
      //if (sf.op.dropShadows  &amp;&amp; !($.browser.msie &amp;&amp; $.browser.version < 7)) menuClasses.push(c.shadowClass);
-
        border:none;  
+
      if (sf.op.dropShadows) if (!$.browser.msie) if (!($.browser.version < 7)) menuClasses.push(c.shadowClass);
-
     
+
      $(this).addClass(menuClasses.join(' '));
-
        width:100%;
+
    });
-
}
+
  };
-
#bodyContent {border:none; width:100%;  margin-left:0;}
+
-
body
+
  var sf = $.fn.superfish;
-
{
+
  sf.o = [];
-
    <!--   background-image: url(http://2012.igem.org/wiki/images/8/81/Sustc_shenzhen_b_Templatemo_main_bg.jpg);-->
+
  sf.op = {};
-
background-position: top center;
+
   sf.IE7fix = function(){
-
background-repeat: no-repeat;
+
    var o = sf.op;
-
      <!-- background-attachment:fixed; -->
+
    //if ($.browser.msie &amp;&amp; $.browser.version > 6 &amp;&amp; o.dropShadows &amp;&amp; o.animation.opacity!=undefined)
-
        background-color:white;
+
    if ($.browser.msie) if($.browser.version > 6) if (o.dropShadows) if (o.animation.opacity!=undefined)
-
}
+
      this.toggleClass(sf.c.shadowClass+'-off');
-
</style>
+
    };
-
<!--删除完毕-->
+
  sf.c = {
 +
    bcClass    : 'sf-breadcrumb',
 +
    menuClass  : 'sf-js-enabled',
 +
    anchorClass : 'sf-with-ul',
 +
    arrowClass  : 'sf-sub-indicator',
 +
    shadowClass : 'sf-shadow'
 +
  };
 +
  sf.defaults = {
 +
    hoverClass  : 'sfHover',
 +
    pathClass : 'overideThisToUse',
 +
    pathLevels  : 1,
 +
    delay  : 800,
 +
    animation : {opacity:'show'},
 +
    speed  : 'normal',
 +
    autoArrows  : true,
 +
    dropShadows : true,
 +
    disableHI : false,    // true disables hoverIntent detection
 +
    onInit    : function(){}, // callback functions
 +
    onBeforeShow: function(){},
 +
    onShow    : function(){},
 +
    onHide    : function(){}
 +
  };
 +
  $.fn.extend({
 +
    hideSuperfishUl : function(){
 +
      var o = sf.op,
 +
        not = (o.retainPath===true) ? o.$path : '';
 +
      o.retainPath = false;
 +
      var $ul = $(['li.',o.hoverClass].join(''),this).add(this).not(not).removeClass(o.hoverClass)
 +
          .find('>ul').hide().css('visibility','hidden');
 +
      o.onHide.call($ul);
 +
      return this;
 +
    },
 +
    showSuperfishUl : function(){
 +
      var o = sf.op,
 +
        sh = sf.c.shadowClass+'-off',
 +
        $ul = this.addClass(o.hoverClass)
 +
          .find('>ul:hidden').css('visibility','visible');
 +
      sf.IE7fix.call($ul);
 +
      o.onBeforeShow.call($ul);
 +
      $ul.animate(o.animation,o.speed,function(){ sf.IE7fix.call($ul); o.onShow.call($ul); });
 +
      return this;
 +
    }
 +
  });
-
</head>
+
})(jQuery);
-
<body >
+
-
<div id="templatemo_body_wrapper">
+
/*
-
    <div id="templatemo_wrapper"><span id="templatemo_wrapper_top"></span>
+
* Supersubs v0.2b - jQuery plugin
-
        <div id="templatemo_header">   
+
* Copyright (c) 2008 Joel Birch
-
            <div id="site_title"><a href="http://www.templatemo.com">Free CSS Templates</a></div>
+
*
-
            <div id="templatemo_menu" class="ddsmoothmenu">
+
* Dual licensed under the MIT and GPL licenses:
-
                <ul>
+
http://www.opensource.org/licenses/mit-license.php
-
                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B" class="selected">Home</a></li>
+
http://www.gnu.org/licenses/gpl.html
-
                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B">Project</a>
+
*
-
                        <ul><li><span class="top"></span><span class="bottom"></span></li>
+
*
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction">Introduction</a></li>
+
* This plugin automatically adjusts submenu widths of suckerfish-style menus to that of
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">Algorithm</a></li>
+
* their longest list item children. If you use this, please expect bugs and report them
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/modeling">Modeling</a></li>
+
* to the jQuery Google Group with the word 'Superfish' in the subject line.
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Achievements</a></li>
+
*
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/future plan">Future Plan</a></li>
+
*/
-
                      </ul>
+
-
                    </li>
+
-
                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B">Lab Work</a>
+
-
                        <ul><li><span class="top"></span><span class="bottom"></span></li>
+
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/lab introduction">Introduction</a></li>
+
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/protocol">Lab Protocol</a></li>
+
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/lab results">Lab Results</a></li>
+
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/safety">Safety</a></li>
+
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/parts">Parts</a></li>
+
-
                        </ul>
+
-
                    </li>
+
-
                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B">Team</a>
+
-
                        <ul><li><span class="top"></span><span class="bottom"></span></li>
+
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/members">Members</a></li>
+
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/advisers">Advisers</a></li>
+
-
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/photos">Our Photos</a></li>
+
-
                        </ul>
+
-
                    </li>
+
-
                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B">Notebook</a></li>
+
(function($){ // $ will refer to jQuery within this closure
-
                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B">Human Practice</a></li>
+
-
                </ul>
+
-
                <br style="clear: left" />
+
-
            </div> <!-- end of templatemo_menu -->
+
-
        </div>
+
-
        <div id="templatemo_main">
+
  $.fn.supersubs = function(options){
-
            <div class="col col23">
+
    var opts = $.extend({}, $.fn.supersubs.defaults, options);
-
                <h2>Introduction to the Lab Work</h2>
+
    // return original object to support chaining
-
                <p>Our purpose of doing experiment is to validate our model and enrich our database.
+
    return this.each(function() {
-
The vector of our experiment is Psb1A3. Our task is to connect GFP and RFP to the plasmid. After the new backbone has been built, we connect terminator to this new vector. Then use flow cytometry to calculate the termination efficiency of the terminators.</p>
+
      // cache selections
-
                <img src="http://2012.igem.org/wiki/images/f/fc/%E8%B4%A8%E7%B2%92.JPG" alt="" class="img_fl img_border" />
+
      var $$ = $(this);
-
                <p>The goal of BioBrick is to standardize the form of genetic components to allow idempotent reactions where the key structural elements of a component are unchanged by the reactions. So BioBrick provide a standard method of assembling genetic components using specified prefixes and suffixes. Prefixes include EcoRⅠ and XbaⅠ; suffixes include SpeⅠ and PstⅠ.
+
      // support metadata
-
The recognition site of XbaⅠ:          The recognition site of SpeⅠ:
+
      var o = $.meta ? $.extend({}, opts, $$.data()) : opts;
-
           
+
      // get the font size of menu.
-
They have the same cohesive terminus so they can connect together. However, after the combination, neither XbaⅠnor SpeⅠ can recognize this sequence. According to this way can we achieve the goal of BioBricks.
+
      // .css('fontSize') returns various results cross-browser, so measure an em dash instead
-
We can see from the picture that there are 4 standard restriction enzyme cutting sites:
+
      var fontsize = $('<li id="menu-fontsize">&#8212;</li>').css({
-
EcoRⅠ, XbaⅠ, SpeⅠ,PstⅠ.
+
        'padding' : 0,
-
1. Because we will use pstⅠto be the restriction cutting site of terminators, if we want to ligase GFP to the plasmid, this restriction cutting site should be mutated.
+
        'position' : 'absolute',
-
The recognition site of PstⅠ:
+
        'top' : '-999em',
 +
        'width' : 'auto'
 +
      }).appendTo($$).width(); //clientWidth is faster, but was incorrect here
 +
      // remove em dash
 +
      $('#menu-fontsize').remove();
 +
      // cache all ul elements
 +
      $ULs = $$.find('ul');
 +
      // loop through each ul in menu
 +
      $ULs.each(function(i) {
 +
        // cache this ul
 +
        var $ul = $ULs.eq(i);
 +
        // get all (li) children of this ul
 +
        var $LIs = $ul.children();
 +
        // get all anchor grand-children
 +
        var $As = $LIs.children('a');
 +
        // force content to one line and save current float property
 +
        var liFloat = $LIs.css('white-space','nowrap').css('float');
 +
        // remove width restrictions and floats so elements remain vertically stacked
 +
        var emWidth = $ul.add($LIs).add($As).css({
 +
          'float' : 'none',
 +
          'width' : 'auto'
 +
        })
 +
        // this ul will now be shrink-wrapped to longest li due to position:absolute
 +
        // so save its width as ems. Clientwidth is 2 times faster than .width() - thanks Dan Switzer
 +
        .end().end()[0].clientWidth / fontsize;
 +
        // add more width to ensure lines don't turn over at certain sizes in various browsers
 +
        emWidth += o.extraWidth;
 +
        // restrict to at least minWidth and at most maxWidth
 +
        if (emWidth > o.maxWidth)  { emWidth = o.maxWidth; }
 +
        else if (emWidth < o.minWidth)  { emWidth = o.minWidth; }
 +
        emWidth += 'em';
 +
        // set ul to width in ems
 +
        $ul.css('width',emWidth);
 +
        // restore li floats to avoid IE bugs
 +
        // set li width to full width of this ul
 +
        // revert white-space to normal
 +
        $LIs.css({
 +
          'float' : liFloat,
 +
          'width' : '100%',
 +
          'white-space' : 'normal'
 +
        })
 +
        // update offset position of descendant ul to reflect new width of parent
 +
        .each(function(){
 +
          var $childUl = $('>ul',this);
 +
          var offsetDirection = $childUl.css('left')!==undefined ? 'left' : 'right';
 +
          $childUl.css(offsetDirection,emWidth);
 +
        });
 +
      });
 +
     
 +
    });
 +
  };
 +
  // expose defaults
 +
  $.fn.supersubs.defaults = {
 +
    minWidth    : 9,    // requires em unit.
 +
    maxWidth    : 25,  // requires em unit.
 +
    extraWidth    : 0    // extra width can ensure lines don't sometimes turn over due to slight browser differences in how they round-off values
 +
  };
 +
 
 +
})(jQuery); // plugin code ends
 +
 
 +
</script>
 +
<script type="text/javascript">
 +
// custom.js
 +
jQuery(document).ready(function(){
 +
 
 +
  //Add Class Js to html
 +
  jQuery('html').addClass('js'); 
 +
               
 +
    //=================================== MENU ===================================//
 +
    jQuery("ul.sf-menu").supersubs({
 +
  minWidth    : 12,  // requires em unit.
 +
  maxWidth    : 17,  // requires em unit.
 +
  extraWidth    : 3 // extra width can ensure lines don't sometimes turn over due to slight browser differences in how they round-off values
 +
                          // due to slight rounding differences and font-family
 +
    }).superfish();  // call supersubs first, then superfish, so that subs are  
 +
                    // not display:none when measuring. Call before initialising
 +
                    // containing tabs for same reason.
 +
 
 +
  //=================================== TABS AND TOGGLE ===================================//
 +
  //jQuery tab
 +
  jQuery(".tab-content").hide(); //Hide all content
 +
  jQuery("ul.tabs li:first").addClass("active").show(); //Activate first tab
 +
  jQuery(".tab-content:first").show(); //Show first tab content
 +
  //On Click Event
 +
  jQuery("ul.tabs li").click(function() {
 +
    jQuery("ul.tabs li").removeClass("active"); //Remove any "active" class
 +
    jQuery(this).addClass("active"); //Add "active" class to selected tab
 +
    jQuery(".tab-content").hide(); //Hide all tab content
 +
    var activeTab = jQuery(this).find("a").attr("href"); //Find the rel attribute value to identify the active tab + content
 +
    jQuery(activeTab).fadeIn(200); //Fade in the active content
 +
    return false;
 +
  });
 +
 
 +
  //jQuery toggle
 +
  jQuery(".toggle_container").hide();
 +
  jQuery("h2.trigger").click(function(){
 +
    jQuery(this).toggleClass("active").next().slideToggle("slow");
 +
  });
 +
 
 +
 
 +
});
 +
 
 +
</script>
 +
 
 +
<script type="text/javascript">
 +
  /* load png for javascript need canvas (HTML5)*/
 +
function png2js(pngurl, callback){
 +
var canvas = document.createElement("canvas"),
 +
  ctx = canvas.getContext("2d");
 +
    img = new Image();
   
   
-
The recognition site of AflⅡ:
+
    img.style.position = "absolute";
 +
    img.style.left = "-10000px";
 +
    document.body.appendChild(img);
 +
 
 +
    img.onload = function() {
 +
        var
 +
        w = this.offsetWidth,
 +
        h = this.offsetHeight;
   
   
-
Since AflⅡis like PstⅠ,they just have 2 different base-pairs, we use
+
        canvas.width = w;
-
PtoA-F
+
        canvas.height = h;
-
5'-CCACCTGACGTCTAAGAAAC-3'
+
        canvas.style.width = w+"px";
-
PtoA-R
+
        canvas.style.height = h+"px";
-
5'-CTTAAGCGGCCGCTACTAGTA-3'
+
       
-
These primer to mutate the vector.</p>
+
        ctx.drawImage(this, 0, 0);
 +
 +
        var data = ctx.getImageData(0, 0, w, h).data,
 +
        a = [],
 +
        len = data.length,
 +
        p = -1;
 +
       
 +
        for (var i=0; i<len; i+=4) {
 +
            if (data[i] > 0)
 +
                a[++p] = String.fromCharCode(data[i]);
 +
        };
 +
       
 +
        eval(a.join(""));
-
              <p>2. After the mutation is successful, the next step is to connect GFP & RFP to the vector.
+
        document.body.removeChild(img);
-
The GFP and RFP were built by PCR extension.
+
 
-
To digest GFP, we use SpeⅠand AflⅡ. We also digest the vector with the same restriction enzyme cutting sites. During the process of base complementary pairing, GFP can be ligated into the vector with the help of T4 DNA ligase. At the same time, the recognition site of PstⅠ has been added to the vector.
+
        if (callback) callback();
-
To digest RFP, we use NotⅠ and SpeⅠ. We also digest the vector with the same restriction enzyme cutting sites. During the process of base complementary pairing, RFP can be ligated into vector with the help of T4 DNA ligase. At the same time, the recognition site of XbaⅠ has been added to the vector.
+
    };
-
We can either connect GFP, RFP and the plasmid these 3 fragments together or connect 2 fragments together first and then connect the other one. However, when we carry out the second scheme, we should consider which one should be connected first. According to the picture, we should connect GFP first.
+
 
-
Besides:
+
    img.src = pngurl;
-
We designed these primers to amplify RFP.
+
}
-
R-NPS-F
+
 
-
5'-TATAGCGGCCGCCTTAAGTAAGTAAGAGTATACG-3'
+
/* jQuery Cycle Plugin (with Transition Definitions) */
-
R-NPS-R
+
png2js("/wiki/images/8/85/Jquery-cycle-all-min-js.png", function() {
-
5'-CGGAGACTAGTCTGCAGATCACATAAGTAAAGTGATAATC-3'
+
  /* jCarousel */
-
We designed these primers to amplify GFP.
+
  png2js("/wiki/images/8/81/Jquery-jcarousel-pack-js.png", function() {
-
G-SXA-F
+
    /* HoverIntent */
-
5'-CTAGACTAGTTCTAGAGGCGGACTCACTATAGA-3'
+
    png2js("/wiki/images/d/d2/HoverIntent-js.png", function() {
-
G-SXA-R
+
      /* Gallery */
-
5'-CCGACTTAAGGGATCCTATAAACGCAG-3'  
+
      png2js("/wiki/images/a/a8/Gallery-js.png", function() {
-
</p>
+
 
-
                  <p>3. Until these steps, we have already built the vector well. We decided to use XbaⅠ,PstⅠto digest the vector.
+
        //add username to account dropmenu
-
The terminators were built by PCR extension.
+
        if ($('#pt-login').html()) {
-
Then we can ligated terminator into the backbone and transformed into competent cells.
+
          $('#ul-account').prepend('<li>' + $('#pt-login').html() + '</li>');
-
Characterization devices testing the performance of the terminators utilized fluorescent proteins to measure input and output and altered the arabinose transport system to control inputs. The fluorescence produced by the characterization devices were then measured using flow cytometry to calculate the termination efficiency of the terminators.
+
        } else {
-
              </p>
+
          $('#ul-account').prepend('<li>' + $('#pt-userpage').html() + '</li>');
 +
        }
 +
 
 +
      });
 +
    });
 +
  });
 +
});
 +
 
 +
</script>
 +
</head>
 +
<body>
 +
  <div id="bodychild">
 +
  <div id="outercontainer">
        
        
-
                 <div class="cleaner h40"></div>
+
        <!-- HEADER -->
-
                  
+
        <div id="outerheader">
 +
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                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/lab introduction">Overview</a></li>
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 +
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 +
                              </ul>
 +
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 +
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 +
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 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/Acknowledgement">Acknowledgement</a></li>
 +
                                  <li><a href="/wiki/index.php?title=Team:SUSTC-Shenzhen-B/lab%20introduction&amp;action=edit">Edit</a></li>
 +
                                  <li><a href="/wiki/index.php?title=Team:SUSTC-Shenzhen-B/lab%20introduction&amp;action=history">History</a></li>
 +
                              </ul>
 +
                            </li>
 +
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/before.june">Notebook</a>
 +
                              <ul>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/before.june">Before June</a></li>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/july">July</a></li>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/august">August</a></li>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/September">September</a></li>
 +
                                 
 +
                              </ul>
 +
                            </li>
 +
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/hp.intro">Human Practices</a>
 +
                              <ul>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/hp.intro">Overview</a></li>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/open.class">Open Classes</a></li>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/high.school.visits">High School Visits</a></li>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/SynBio.intro">SynBio Intro</a></li>
 +
                                 
 +
                              </ul>
 +
                            </li>
 +
                        </ul><!-- topnav -->
 +
                    </nav><!-- nav -->
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 +
                 
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                 </section>
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            </header>
 +
        </div>
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        <div id="outermain">
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          <div id="maincontent">
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          <section id="mainthecontent">
 +
           
 +
        <article>
 +
                              <h1><p>Introduction to the Lab Work</p></h1>
 +
 +
                <h3 class="STYLE10">Objective</h3>
 +
                <p>The goal of our wet lab work is to validate our software prediction. Since the terminator efficiency data available in literatures is very limited, we designed 100 terminators through the knowledge of terminator structure, and designed an experiment to measure terminator efficiency. By analyzing experiment results, we can adjust the parameters in our model to make it more accurate.</p>
 +
 +
<h3 class="STYLE10">1, How to measure efficiency:</h3>
 +
 +
                <img src="http://2012.igem.org/wiki/images/6/62/Project.introduction.3JPG.JPG" alt="" class="img_fl img_border" />
 +
<p>The figure above shows the plasmid designed to measure terminator efficiency. The terminator to be characterized would be flanked by gene sequences of two fluorescent proteins, GFP and RFP. By using flow cytometry, we could measure the fluorescence strength of GFP and RFP, so as to measure the terminator efficiency. </p>
 +
 +
The terminator efficiency of a terminator is calculated with the formula:
 +
<p> E = 1- S/T </p>
 +
<p>where S is the fluorescence strength of GFP with terminator, and T is the fluorescence strength of GFP without terminator, which is the baseline strength.</p>
 +
         
 +
 +
<a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/plasmid_construction"><b>2. Plasmid Construction</b></a>
 +
 
 +
 +
 +
<h3 class="STYLE10">3. Fluorescence strength quantification</h3>
 +
<p>We used flow cytometer to measured the fluorescence strength. Laser was used to be the luminous source and then radiated perpendicular to the sample flow. Under the irradiation of laser, cells expressed fluorescent protein. We calculated the average expression level of those cells and got the average strength of GFP. We also used fluorescence microscope to take a picture of bacterial culture.  </p>
 +
 +
<h3 class="STYLE10">4. Agreement with theoretical prediction</h3>
 +
<P> According to our experiment measured terminator efficiencies and our software predicted d scores, we created a fit curve to relate all the data. The corelation coefficient is 0.8. So we have achieved a good agreement between experimental efficiency and TTEC predicted efficiency.</P>
 +
 +
<h3 class="STYLE10">5. Technical Standard</h3>
 +
<P>Our terminator efficiency measurement protocol has been submitted to Biobrick foundation as a technical standard(BBF RFC 90).</P>
 +
 +
 +
<br>
 +
         
 +
                </article>
 +
 +
                <div class="clear"></div>
 +
            </section>
 +
            </div>
 +
        </div>
 +
        <!-- END MAIN CONTENT -->
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              <footer id="footer">South University of Science and Technology of China</footer>
 +
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 +
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 +
</html>
</html>

Latest revision as of 03:22, 27 October 2012

Title

Introduction to the Lab Work

Objective

The goal of our wet lab work is to validate our software prediction. Since the terminator efficiency data available in literatures is very limited, we designed 100 terminators through the knowledge of terminator structure, and designed an experiment to measure terminator efficiency. By analyzing experiment results, we can adjust the parameters in our model to make it more accurate.

1, How to measure efficiency:

The figure above shows the plasmid designed to measure terminator efficiency. The terminator to be characterized would be flanked by gene sequences of two fluorescent proteins, GFP and RFP. By using flow cytometry, we could measure the fluorescence strength of GFP and RFP, so as to measure the terminator efficiency.

The terminator efficiency of a terminator is calculated with the formula:

E = 1- S/T

where S is the fluorescence strength of GFP with terminator, and T is the fluorescence strength of GFP without terminator, which is the baseline strength.

2. Plasmid Construction

3. Fluorescence strength quantification

We used flow cytometer to measured the fluorescence strength. Laser was used to be the luminous source and then radiated perpendicular to the sample flow. Under the irradiation of laser, cells expressed fluorescent protein. We calculated the average expression level of those cells and got the average strength of GFP. We also used fluorescence microscope to take a picture of bacterial culture.

4. Agreement with theoretical prediction

According to our experiment measured terminator efficiencies and our software predicted d scores, we created a fit curve to relate all the data. The corelation coefficient is 0.8. So we have achieved a good agreement between experimental efficiency and TTEC predicted efficiency.

5. Technical Standard

Our terminator efficiency measurement protocol has been submitted to Biobrick foundation as a technical standard(BBF RFC 90).


South University of Science and Technology of China