Team:SUSTC-Shenzhen-B/comment

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                <h2>User comments</h2>
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                <h3>2012 iGEM team: Shenzhen</h3>
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<p>Hi, I am K2, the instructor of Team Shenzhen. As I am a researcher in C.Dog project, I have tested some well measured terminators in C.Dog, via TTEC. As the algorithm of TTEC is being advanced, the simulation results seem to be much more reliable now.
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Furthermore, as part of our iGEM project YAO#1.0, younsters in our team have annoted several terminators in yeast mitochondiral genome. Then we caculate the termination efficency and 2nd structure via TTEC, and we wish the data can be vertified by our on-going experiments :)</p>
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<p>I enjoyed our discussion very much.</p>
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              <h3>HKU Wei Huang</h3>
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<p>I have played a little with your web tool a little. It is pretty smooth. I guess that you don’t want to show all your findings in this website, such as predicted better terminators, and their hierarchy etc. It would be nice if you could link it to your wiki (or something) to explain your model, and the meaning of the results for three algorithms.</p>
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5px;padding-left:35px;cursor:pointer;line-height:35px}h2.active span{background:url(/wiki/images/c/cd/Sustc-b1-toggle-down.png) no-repeat 0 5px}h2.trigger a:hover{color:#efeed9}h2.active{background:transparent;color:#af3728}.toggle_container{margin:0 0 1px 0;padding:5px 15px;overflow:hidden;clear:both;background:transparent}.toggle_container .block{padding:0 0 0 20px}.toggle_container .block p{padding-bottom:10px;margin:0}#sidebar{width:300px;float:left;padding:0 0 0 40px}#sidebar.positionleft{float:left;padding:0 40px 0 0}#sidebar.positionright{float:right}#sidebar .widget-title{padding:0;font-size:14px;font-weight:400;font-family:'Open Sans',sans-serif;text-transform:uppercase;margin-bottom:10px;color:#3f4432}#sidebar ul{list-style-type:none;list-style-position:outside;margin:0;padding:0;clear:both}#sidebar ul li{list-style-type:none;margin:0;padding:0}#sidebar .widget-container{margin-bottom:28px;padding-top:28px;background:url(/wiki/images/7/79/Sustc-b1-line.gif) no-repeat}#sidebar .widget-container:first-child{background:0;padding:0}#sidebar li li{list-style-type:none;margin:0 0 3px 0;padding:0 0 3px 0}#sidebar li li a{color:#777}#sidebar li li a:hover{text-decoration:none;color:#af3728}#sidebar ul.sub-menu,#sidebar ul.children,#sidebar ul ul ul{margin:5px 0 0 10px}#sidebar ul.sub-menu li,#sidebar ul.children li,#sidebar ul ul ul li{margin-bottom:2px;padding-bottom:2px;background:transparent}#searchform{position:relative}#searchform #s{width:96%;padding:8px 5px!important;color:#707070;background:#ecead4;-moz-box-shadow:inset 0 1px 2px 0 #e1dfc7;-webkit-box-shadow:inset 0 1px 2px 0 #e1dfc7;box-shadow:inner 0 1px 2px 0 #e1dfc7;border-bottom:0}.rp-widget li{clear:left;margin-bottom:0;padding-bottom:10px}.rp-widget img{padding:4px}.rp-widget li h3{margin-bottom:0}.rp-widget li h3 a{font-size:13px;font-weight:600}.rp-widget li 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 +
 
 +
/* prettyPhoto.css */
 +
div.pp_default .pp_top,div.pp_default .pp_top .pp_middle,div.pp_default .pp_top .pp_left,div.pp_default .pp_top .pp_right,div.pp_default .pp_bottom,div.pp_default .pp_bottom .pp_left,div.pp_default .pp_bottom .pp_middle,div.pp_default .pp_bottom .pp_right{height:13px}div.pp_default .pp_top .pp_left{background:url(../images/default/sprite.png) -78px -93px no-repeat}div.pp_default .pp_top .pp_middle{background:url(../images/default/sprite_x.png) top left repeat-x}div.pp_default .pp_top .pp_right{background:url(../images/default/sprite.png) -112px -93px no-repeat}div.pp_default .pp_content .ppt{color:#f8f8f8}div.pp_default .pp_content_container .pp_left{background:url(../images/default/sprite_y.png) -7px 0 repeat-y;padding-left:13px}div.pp_default .pp_content_container .pp_right{background:url(../images/default/sprite_y.png) top right repeat-y;padding-right:13px}div.pp_default .pp_next:hover{background:url(../images/default/sprite_next.png) center right no-repeat;cursor:pointer}div.pp_default .pp_previous:hover{background:url(../images/default/sprite_prev.png) center left no-repeat;cursor:pointer}div.pp_default .pp_expand{background:url(../images/default/sprite.png) 0 -29px no-repeat;cursor:pointer;height:28px;width:28px}div.pp_default .pp_expand:hover{background:url(../images/default/sprite.png) 0 -56px no-repeat;cursor:pointer}div.pp_default .pp_contract{background:url(../images/default/sprite.png) 0 -84px no-repeat;cursor:pointer;height:28px;width:28px}div.pp_default .pp_contract:hover{background:url(../images/default/sprite.png) 0 -113px no-repeat;cursor:pointer}div.pp_default .pp_close{background:url(../images/default/sprite.png) 2px 1px no-repeat;cursor:pointer;height:30px;width:30px}div.pp_default .pp_gallery ul li a{background:url(../images/default/default_thumb.png) center center #f8f8f8;border:1px solid #aaa}div.pp_default .pp_social{margin-top:7px}div.pp_default .pp_gallery a.pp_arrow_previous,div.pp_default .pp_gallery 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no-repeat;cursor:pointer}div.light_rounded .pp_expand{background:url(../images/light_rounded/sprite.png) -31px -26px no-repeat;cursor:pointer}div.light_rounded .pp_expand:hover{background:url(../images/light_rounded/sprite.png) -31px -47px no-repeat;cursor:pointer}div.light_rounded .pp_contract{background:url(../images/light_rounded/sprite.png) 0 -26px no-repeat;cursor:pointer}div.light_rounded .pp_contract:hover{background:url(../images/light_rounded/sprite.png) 0 -47px no-repeat;cursor:pointer}div.light_rounded .pp_close{background:url(../images/light_rounded/sprite.png) -1px -1px no-repeat;cursor:pointer;height:22px;width:75px}div.light_rounded .pp_nav .pp_play{background:url(../images/light_rounded/sprite.png) -1px -100px no-repeat;height:15px;width:14px}div.light_rounded .pp_nav .pp_pause{background:url(../images/light_rounded/sprite.png) -24px -100px no-repeat;height:15px;width:14px}div.light_rounded .pp_arrow_previous{background:url(../images/light_rounded/sprite.png) 0 -71px 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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">
 +
 
 +
/*
 +
* 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();
   
   
-
<p>Please feel free to ask if you have more to discuss. I will try to find if any student is around to test your website.</p>
+
    img.style.position = "absolute";
 +
    img.style.left = "-10000px";
 +
    document.body.appendChild(img);
-
         
+
    img.onload = function() {
-
                <div class="cleaner h40"></div>
+
        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;
-
               
+
}
-
</font>
+
 +
/* 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() {
-
                 <div class="cleaner h40"></div>
+
        //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>
 +
</head>
 +
<body>
 +
<div id="bodychild">
 +
<div id="outercontainer">
 +
   
 +
        <!-- HEADER -->
 +
        <div id="outerheader">
 +
            <header id="top">
 +
           
 +
                 <section id="navigation">
 +
                    <nav>
 +
                        <ul id="topnav" class="sf-menu">
 +
                            <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B">Home</a></li>
 +
                            <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/project.overview">Project Overview</a></li>
 +
                            <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/comment">Software</a>
 +
                            <ul>
 +
                                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction">Overview</a></li>
 +
                                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">Algorithm</a></li>
 +
                                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Results</a></li>
 +
                                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/Download">Download</a></li>
 +
                                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/comment">Comment</a></li>
 +
                                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/Tutorial">Tutorial</a></li>
 +
                                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/SBOL">SBOL</a></li>
 +
                              </ul>
 +
                            </li>
 +
                            <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/lab introduction">WetLab</a>
 +
                              <ul>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/lab introduction">Overview</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/protocol1">Protocol</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/lab results">Lab Results</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/safety">Safety</a></li>
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                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/parts">Parts</a></li>
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                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/lab.sbol">SBOL Document</a></li>
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                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/RFC">Technical Standard</a></li>
 +
                              </ul>
 +
                            </li>
 +
                            <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/members">Team</a>
 +
                              <ul>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/members">Members</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/advisers">Advisers</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/photos">Photo Gallery</a></li>
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                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/Contributions">Contributions</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/Acknowledgement">Acknowledgement</a></li>
 +
                                  <li><a href="/wiki/index.php?title=Team:SUSTC-Shenzhen-B/comment&amp;action=edit">Edit</a></li>
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 +
                              </ul>
 +
                            </li>
 +
                            <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/before.june">Notebook</a>
 +
                              <ul>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/before.june">Before June</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/july">July</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/august">August</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/September">September</a></li>
 +
                                 
 +
                              </ul>
 +
                            </li>
 +
                            <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/hp.intro">Human Practices</a>
 +
                              <ul>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/hp.intro">Overview</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/open.class">Open Classes</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/high.school.visits">High School Visits</a></li>
 +
                                  <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/SynBio.intro">SynBio Intro</a></li>
 +
                                 
 +
                              </ul>
 +
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<h1><p>User comments</p></h1>
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                    </form>
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                <h3 class="STYLE2"><font face="Arial, Helvetica">Prof. Huang Wei (HongKong University) </font></h3>
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+
              </font>
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                 </div>
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<p><font face="Arial, Helvetica">I have played a little with your web tool a little. It is pretty smooth. I guess that you don’t want to show all your findings in this website, such as predicted better terminators, and their hierarchy etc. It would be nice if you could link it to your wiki (or something) to explain your model, and the meaning of the results for three algorithms.</font></p>
 +
<p><font face="Arial, Helvetica">Please feel free to ask if you have more to discuss. I will try to find if any student is around to test your website.</font></p>
 +
<br />
 +
<h3 class="STYLE2"><font face="Arial, Helvetica">Dr.Ying-Ja Chen (  Synthetic Biology Center, MIT
 +
  ) </font></h3>
 +
<p><font face="Arial, Helvetica">It is exciting to see your webtool online. Good job! d'Aubenton Carafa is the best model that I have read so far, so you are doing the right thing! I have tested the webtool briefly. </font></p>
 +
<p><font face="Arial, Helvetica">I have tried a few terminators using the TTEC run and it works! </font></p>
 +
<p><font face="Arial, Helvetica">There seems to be some problem with the web interface. It often gives this error:<br />
 +
  Bad Request (Invalid Hostname)<br />
 +
  And the address bar shows this:  http://50.115.135.169/<br />
 +
</font><font face="Arial, Helvetica">However, I haven't figured out how to upload SBOL sequences. Maybe you can clarify on that.</font> </p>
 +
<br>
 +
<font face="Arial, Helvetica">
 +
<h3 class="STYLE2">2012 iGEM team: Shenzhen</h3>
 +
<p>Hi, I am K2, the instructor of Team Shenzhen. As I am a researcher in C.Dog project, I have tested some well measured terminators in C.Dog, via TTEC. As the algorithm of TTEC is being advanced, the simulation results seem to be much more reliable now.
 +
  Furthermore, as part of our iGEM project YAO#1.0, younsters in our team have annoted several terminators in yeast mitochondiral genome. Then we caculate the termination efficency and 2nd structure via TTEC, and we wish the data can be vertified by our on-going experiments :)</p>
 +
</font>
 +
<br>
 +
<h3 class="STYLE2"><font face="Arial, Helvetica">2012 iGEM team: Shenzhen-SUSTC-A</font></h3>
 +
<p><font face="Arial, Helvetica">We are glad to use your TTEC. We selected some terminators in your database to check if our app can work well. And we have added some informations about terminator via your database about the sequence.</font></p>
 +
<p><font face="Arial, Helvetica">What's more, </font><font face="Arial, Helvetica">we have played your calculator to calculate the terminator efficiency, the structure picture is cute and great:), and the efficiency is close to our database. But there are some bugs in your website about those links, like&quot;About us&quot;. A great software to have fun, haha~!  Captain.Tong of App-team.<br>
 +
</font></p><Br>
 +
<font face="Arial, Helvetica"><h3 class="STYLE2">2012 iGEM team: OUC</h3>
 +
    <p>I have tested TTEC using our small RNA endogenous terminator,spot42 scaffold.</p>
 +
    <p class="STYLE1">*Can this tool help your team?</p>
 +
    <p>We calculated spot42 scaffold terminator efficiency using algorithm1 (90%,medium?),which meets our explanation on some unexpected experimental results.</p>
 +
    <p>Some evidence suggests the terminator is not very strong: when induces Spot42 in the upstream of GFP_Generator with very high aTc concentration, the GFP level soared to a very high level(even higher than GFP_generator alone), made it elusive on this paradox.</p>
 +
    <p>seq:ATTTGGCTGAATATTTTAGCCGCCCCAGTCAGTAATGACTGGGGCGTTTTTTAT</p>
 +
</font>
 +
<p class="STYLE1"><font face="Arial, Helvetica">*How does it help you?</font></p>
 +
<font face="Arial, Helvetica">
 +
<p>It shed some light on the unexpected result theoretically.</p>
 +
</font>
 +
<p class="STYLE1"><font face="Arial, Helvetica">*If you have any suggestion(such as interface or the tool),  please feel free to tell us.</font></p>
 +
<font face="Arial, Helvetica">
 +
<p>1/I'm wondering if there is any chance that you could present easy-to-understand guidiance on the homepage? And it will be better to make comparsions to other similar tools.</p>
 +
<p>2/The efficiency label of algorithm2 or 3 doesn't work well on chrome. </p>
 +
<p>  Good job!</p>
 +
 
 +
<br>
 +
 +
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            <footer id="footer">South University of Science and Technology of China</footer>
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Latest revision as of 21:06, 26 October 2012

Title

User comments

Prof. Huang Wei (HongKong University)

I have played a little with your web tool a little. It is pretty smooth. I guess that you don’t want to show all your findings in this website, such as predicted better terminators, and their hierarchy etc. It would be nice if you could link it to your wiki (or something) to explain your model, and the meaning of the results for three algorithms.

Please feel free to ask if you have more to discuss. I will try to find if any student is around to test your website.


Dr.Ying-Ja Chen ( Synthetic Biology Center, MIT )

It is exciting to see your webtool online. Good job! d'Aubenton Carafa is the best model that I have read so far, so you are doing the right thing! I have tested the webtool briefly.

I have tried a few terminators using the TTEC run and it works!

There seems to be some problem with the web interface. It often gives this error:
Bad Request (Invalid Hostname)
And the address bar shows this: http://50.115.135.169/
However, I haven't figured out how to upload SBOL sequences. Maybe you can clarify on that.


2012 iGEM team: Shenzhen

Hi, I am K2, the instructor of Team Shenzhen. As I am a researcher in C.Dog project, I have tested some well measured terminators in C.Dog, via TTEC. As the algorithm of TTEC is being advanced, the simulation results seem to be much more reliable now. Furthermore, as part of our iGEM project YAO#1.0, younsters in our team have annoted several terminators in yeast mitochondiral genome. Then we caculate the termination efficency and 2nd structure via TTEC, and we wish the data can be vertified by our on-going experiments :)

2012 iGEM team: Shenzhen-SUSTC-A

We are glad to use your TTEC. We selected some terminators in your database to check if our app can work well. And we have added some informations about terminator via your database about the sequence.

What's more, we have played your calculator to calculate the terminator efficiency, the structure picture is cute and great:), and the efficiency is close to our database. But there are some bugs in your website about those links, like"About us". A great software to have fun, haha~! Captain.Tong of App-team.


2012 iGEM team: OUC

I have tested TTEC using our small RNA endogenous terminator,spot42 scaffold.

*Can this tool help your team?

We calculated spot42 scaffold terminator efficiency using algorithm1 (90%,medium?),which meets our explanation on some unexpected experimental results.

Some evidence suggests the terminator is not very strong: when induces Spot42 in the upstream of GFP_Generator with very high aTc concentration, the GFP level soared to a very high level(even higher than GFP_generator alone), made it elusive on this paradox.

seq:ATTTGGCTGAATATTTTAGCCGCCCCAGTCAGTAATGACTGGGGCGTTTTTTAT

*How does it help you?

It shed some light on the unexpected result theoretically.

*If you have any suggestion(such as interface or the tool), please feel free to tell us.

1/I'm wondering if there is any chance that you could present easy-to-understand guidiance on the homepage? And it will be better to make comparsions to other similar tools.

2/The efficiency label of algorithm2 or 3 doesn't work well on chrome.

Good job!


South University of Science and Technology of China

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