Template:SUSTC-B1

From 2012.igem.org

(Difference between revisions)
 
(71 intermediate revisions not shown)
Line 19: Line 19:
#catlinks {display:none; }
#catlinks {display:none; }
#footer-box {display:none; }
#footer-box {display:none; }
-
/* #menubar {display:none; } */
+
#menubar {display:none; }
/* googleapis-font */
/* googleapis-font */
Line 52: Line 52:
</style>
</style>
<script type="text/javascript">
<script type="text/javascript">
 +
 +
/*
 +
* Superfish v1.4.8 - jQuery menu widget
 +
* Copyright (c) 2008 Joel Birch
 +
*
 +
* Dual licensed under the MIT and GPL licenses:
 +
* 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
 +
*/
 +
 +
;(function($){
 +
$.fn.superfish = function(op){
 +
 +
var sf = $.fn.superfish,
 +
c = sf.c,
 +
$arrow = $(['<span class="',c.arrowClass,'"> &#187;</span>'].join('')),
 +
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;
 +
}
 +
 +
$('li:has(ul)',this)[(bcheck) ? 'hoverIntent' : 'hover'](over,out).each(function() {
 +
if (o.autoArrows) addArrow( $('>a:first-child',this) );
 +
})
 +
.not('.'+c.bcClass)
 +
.hideSuperfishUl();
 +
 +
var $a = $('a',this);
 +
$a.each(function(i){
 +
var $li = $a.eq(i).parents('li');
 +
$a.eq(i).focus(function(){over.call($li);}).blur(function(){out.call($li);});
 +
});
 +
o.onInit.call(this);
 +
 +
}).each(function() {
 +
var menuClasses = [c.menuClass];
 +
//if (sf.op.dropShadows  &amp;&amp; !($.browser.msie &amp;&amp; $.browser.version < 7)) menuClasses.push(c.shadowClass);
 +
if (sf.op.dropShadows) if (!$.browser.msie) if (!($.browser.version < 7)) menuClasses.push(c.shadowClass);
 +
$(this).addClass(menuClasses.join(' '));
 +
});
 +
};
 +
 +
var sf = $.fn.superfish;
 +
sf.o = [];
 +
sf.op = {};
 +
sf.IE7fix = function(){
 +
var o = sf.op;
 +
//if ($.browser.msie &amp;&amp; $.browser.version > 6 &amp;&amp; o.dropShadows &amp;&amp; o.animation.opacity!=undefined)
 +
if ($.browser.msie) if($.browser.version > 6) if (o.dropShadows) if (o.animation.opacity!=undefined)
 +
this.toggleClass(sf.c.shadowClass+'-off');
 +
};
 +
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;
 +
}
 +
});
 +
 +
})(jQuery);
 +
 +
/*
 +
* Supersubs v0.2b - jQuery plugin
 +
* Copyright (c) 2008 Joel Birch
 +
*
 +
* Dual licensed under the MIT and GPL licenses:
 +
* http://www.opensource.org/licenses/mit-license.php
 +
* http://www.gnu.org/licenses/gpl.html
 +
*
 +
*
 +
* This plugin automatically adjusts submenu widths of suckerfish-style menus to that of
 +
* their longest list item children. If you use this, please expect bugs and report them
 +
* to the jQuery Google Group with the word 'Superfish' in the subject line.
 +
*
 +
*/
 +
 +
(function($){ // $ will refer to jQuery within this closure
 +
 +
$.fn.supersubs = function(options){
 +
var opts = $.extend({}, $.fn.supersubs.defaults, options);
 +
// return original object to support chaining
 +
return this.each(function() {
 +
// cache selections
 +
var $$ = $(this);
 +
// support metadata
 +
var o = $.meta ? $.extend({}, opts, $$.data()) : opts;
 +
// get the font size of menu.
 +
// .css('fontSize') returns various results cross-browser, so measure an em dash instead
 +
var fontsize = $('<li id="menu-fontsize">&#8212;</li>').css({
 +
'padding' : 0,
 +
'position' : 'absolute',
 +
'top' : '-999em',
 +
'width' : 'auto'
 +
}).appendTo($$).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();
 +
 +
    img.style.position = "absolute";
 +
    img.style.left = "-10000px";
 +
    document.body.appendChild(img);
 +
 +
    img.onload = function() {
 +
        var
 +
        w = this.offsetWidth,
 +
        h = this.offsetHeight;
 +
 +
        canvas.width = w;
 +
        canvas.height = h;
 +
        canvas.style.width = w+"px";
 +
        canvas.style.height = h+"px";
 +
       
 +
        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(""));
 +
 +
        document.body.removeChild(img);
 +
 +
        if (callback) callback();
 +
    };
 +
 +
    img.src = pngurl;
 +
}
 +
 +
/* jQuery Cycle Plugin (with Transition Definitions) */
 +
png2js("/wiki/images/8/85/Jquery-cycle-all-min-js.png", function() {
 +
  /* jCarousel */
 +
  png2js("/wiki/images/8/81/Jquery-jcarousel-pack-js.png", function() {
 +
    /* HoverIntent */
 +
    png2js("/wiki/images/d/d2/HoverIntent-js.png", function() {
 +
      /* Gallery */
 +
      png2js("/wiki/images/a/a8/Gallery-js.png", function() {
 +
 +
        //add username to account dropmenu
 +
        if ($('#pt-login').html()) {
 +
          $('#ul-account').prepend('<li>' + $('#pt-login').html() + '</li>');
 +
        } else {
 +
          $('#ul-account').prepend('<li>' + $('#pt-userpage').html() + '</li>');
 +
        }
 +
 +
      });
 +
    });
 +
  });
 +
});
 +
</script>
</script>
</head>
</head>
Line 65: Line 394:
                     <nav>
                     <nav>
                         <ul id="topnav" class="sf-menu">
                         <ul id="topnav" class="sf-menu">
-
                             <li><a href="index.html" class="current">Home</a></li>
+
                             <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B">Home</a></li>
-
                             <li><a href="about.html">About</a>
+
                             <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction">Software</a>
                             <ul>
                             <ul>
-
                                <li><a href="element.html">Element</a></li>
+
                                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction">Overview</a></li>
-
                                     <li><a href="single.html">Blog Detail</a></li>
+
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">Algorithm</a></li>
-
                                     <li><a href="accommodation-details.html">Accommodation Details</a></li>
+
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Achievements</a></li>
-
                                </ul>
+
                                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/Download">Download</a></li>
 +
                                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/comment">Comment</a></li>
 +
                                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/Tutorial">Tutorial</a></li>
 +
                                    <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/SBOL">SBOL</a></li>
 +
                              </ul>
 +
                            </li>
 +
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/lab introduction">WetLab</a>
 +
                              <ul>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/lab introduction">Overview</a></li>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/protocol1">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>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/lab.sbol">SBOL Document</a></li>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/RFC">Technical Standard</a></li>
 +
                              </ul>
 +
                            </li>
 +
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/members">Team</a>
 +
                              <ul>
 +
                                  <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">Photo Gallery</a></li>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/Contributions">Contributions</a></li>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/Acknowledgement">Acknowledgement</a></li>
 +
                                  <li><a href="/wiki/index.php?title=Template:SUSTC-B1&amp;action=edit">Edit</a></li>
 +
                                  <li><a href="/wiki/index.php?title=Template:SUSTC-B1&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>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/October">October</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>
 +
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/October">October</a></li>
 +
                              </ul>
                             </li>
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                                <h1>Transcriptional Terminator Efficiency Calculator (TTEC)</h1>
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<h1>Welcome</h1>
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<p>We studied the rho-independent transcription terminators which regulate gene expression using both theoretical model and experiment method.</p>
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<p> We first developed a theoretical model. This model calculated the free energy of RNA folding and could predict the secondary structure of terminators. From the secondary structure, we proposed an algorithm that can predict terminator efficiency.</p>
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<p> To validate our theoretical prediction, we also perform wetlab experiments. We construct 100 terminators. We measure the the terminator efficiency by measuring the GFP and RFP which are placed before and after terminators.</p>
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<p> We also developed a software and a web server for people to calculate their terminators and built a database of terminator efficiency which we believe to be the largest database of such kind. Our work is by far the most comprehensive study on terminator efficiency.</p>
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Latest revision as of 15:07, 25 October 2012

Title



Transcriptional Terminator Efficiency Calculator (TTEC)

We studied the rho-independent transcription terminators which regulate gene expression using both theoretical model and experiment method.

We first developed a theoretical model. This model calculated the free energy of RNA folding and could predict the secondary structure of terminators. From the secondary structure, we proposed an algorithm that can predict terminator efficiency.

To validate our theoretical prediction, we also perform wetlab experiments. We construct 100 terminators. We measure the the terminator efficiency by measuring the GFP and RFP which are placed before and after terminators.

We also developed a software and a web server for people to calculate their terminators and built a database of terminator efficiency which we believe to be the largest database of such kind. Our work is by far the most comprehensive study on terminator efficiency.

South University of Science and Technology of China

Retrieved from "http://2012.igem.org/Template:SUSTC-B1"