Team:TPHS SanDiego/Project

From 2013hs.igem.org

(Difference between revisions)
Line 278: Line 278:
</html>
</html>
-
<html lang="en">  
+
<html>
-
<style = "text/css" media="screen">
+
<script type="text/javascript">
-
 
-
 
-
 
-
ul.topnav {
 
-
list-style: none;
 
-
padding: 0px 0px;
 
-
margin: 0px 0px 0px -22px;
 
-
width:1000px;
 
-
float: left;
 
-
 
-
 
-
 
-
}
 
-
ul.topnav li {
 
-
font-family: 'Georgia', Times, serif;
 
-
font-weight: 150;
 
-
font-size: 1.65em;
 
-
float: left;
 
-
margin:0px 0px 0px 0px;
 
-
opacity:.8;
 
-
padding: 2px 6px 10px 12px;
 
-
position: 0px 0px; /*--Declare X and Y axis base for sub navigation--*/
 
-
}
 
-
ul.topnav li a{
 
-
padding: 18px 8px 10px 10px;
 
-
color: white;
 
-
display: block;
 
-
 
-
 
-
 
-
text-decoration: none;
 
-
float: left;
 
-
}
 
-
ul.topnav li a:hover{
 
-
background-color:black;
 
-
padding: 18px 8px 10px 10px;
 
-
font-color: white;
 
-
 
-
}
 
-
ul.topnav li span { /*--Drop down trigger styles--*/
 
-
width: 17px;
 
-
height: 25px;
 
-
 
-
float: left;
 
-
background-color: gray;
 
-
}
 
-
ul.topnav li span.subhover {background-position: center bottom; cursor: pointer;} /*--Hover effect for trigger--*/
 
-
ul.topnav li ul.subnav {
 
-
list-style: none;
 
-
position: absolute; /*--Important - Keeps subnav from affecting main navigation flow--*/
 
-
left: 3px; top: 55px;
 
-
background: #333;
 
-
margin: 0; padding: 3px;
 
-
display: none;
 
-
float: left;
 
-
width: 160px;
 
-
opacity: .6;
 
-
border: 1px solid #111;
 
-
}
 
-
ul.topnav li ul.subnav li{
 
-
margin: 0; padding: 0;
 
-
border-top: 1px solid #252525; /*--Create bevel effect--*/
 
-
border-bottom: 1px solid #444; /*--Create bevel effect--*/
 
-
clear: both;
 
-
height:45px;
 
-
width: 155px;
 
-
font-size: .5em;
 
-
font-family: 'Georgia', Times, serif;
 
-
font-weight: 150;
 
-
 
-
 
-
}
 
-
html ul.topnav li ul.subnav li a {
 
-
float: left;
 
-
height:25px;
 
-
width: 145px;
 
-
background-color: white;
 
-
padding-left: 3px;
 
-
 
-
}
 
-
html ul.topnav li ul.subnav li a:hover { /*--Hover effect for subnav links--*/
 
-
background-color: blue;
 
-
}
 
-
 
-
 
-
#content1{
 
-
font-family:Georgia ,Helvetica,sans-serif;
 
-
height: 300px;
 
-
  }
 
-
 
-
#content2{
 
-
font-family:Georgia ,Helvetica,sans-serif;
 
-
height: 50px;
 
-
  }
 
-
body{ background: url(https://static.igem.org/mediawiki/2013hs/f/f4/BackgroundTareq.jpg);}
 
-
#globalWrapper {width: 100%;}
 
-
 
-
#content{
 
-
padding: 0px;
 
-
width: 1000px;
 
-
background: #ffe5d4;
 
-
// Background Color
 
-
font-family:Georgia ,Helvetica,sans-serif;
 
-
border: none;
 
-
text-decoration: none;
 
-
 
-
}
 
-
 
-
.main_item h1{
 
-
text-decoration:none;
 
-
}
 
-
 
-
#p-logo{
 
-
display:none;
 
-
}
 
-
 
-
#top-section2{
 
-
width: 100%;
 
-
 
-
background: url(http://www.eecs.berkeley.edu/~jvmiller/images/imagetestberkeley.gif);
 
-
height: 65px;
 
-
}
 
-
#top-section3{
 
-
width: 100%;
 
-
height:78px;
 
-
}
 
-
 
-
 
-
#spacer {
 
-
    height: 20px;
 
-
 
-
}
 
-
 
-
#team{border: 1px solid black;
 
-
padding: 2px;
 
-
height:380px;}
 
-
 
-
 
-
#search-controls{
 
-
display:none;
 
-
}
 
-
 
-
#spacer2 {
 
-
    height: 12em;
 
-
 
-
}
 
-
 
-
#spacer3 {
 
-
    height: .4em;
 
-
 
-
}
 
-
 
-
#top-section{
 
-
width: 100%;
 
-
background: url(https://static.igem.org/mediawiki/2011/6/68/Noise_pattern_8.jpg);
 
-
height: 5px;
 
-
border:none;
 
-
}
 
-
 
-
.firstHeading {
 
-
display:none;
 
-
}
 
/*
/*
-
* jQuery Nivo Slider v2.6
+
* Slides, A Slideshow Plugin for jQuery
-
* http://nivo.dev7studios.com
+
* Intructions: http://slidesjs.com
-
*
+
* By: Nathan Searles, http://nathansearles.com
-
* Copyright 2011, Gilbert Pellegrom
+
* Version: 1.1.8
-
* Free to use and abuse under the MIT license.
+
* Updated: June 1st, 2011
-
* http://www.opensource.org/licenses/mit-license.php
+
*
-
*  
+
* Licensed under the Apache License, Version 2.0 (the "License");
-
* March 2010
+
* you may not use this file except in compliance with the License.
-
*/
+
* You may obtain a copy of the License at
-
+
*
-
+
* http://www.apache.org/licenses/LICENSE-2.0
-
/* The Nivo Slider styles */
+
*
-
.nivoSlider {
+
* Unless required by applicable law or agreed to in writing, software
-
position:relative;
+
* distributed under the License is distributed on an "AS IS" BASIS,
-
        effect: 'fade'
+
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-
}
+
* See the License for the specific language governing permissions and
-
.nivoSlider img {
+
* limitations under the License.
-
position:absolute;
+
*/
-
top:0px;
+
(function(A){A.fn.slides=function(B){B=A.extend({},A.fn.slides.option,B);return this.each(function(){A("."+B.container,A(this)).children().wrapAll('<div class="slides_control"/>');var V=A(this),J=A(".slides_control",V),Z=J.children().size(),Q=J.children().outerWidth(),M=J.children().outerHeight(),D=B.start-1,L=B.effect.indexOf(",")<0?B.effect:B.effect.replace(" ","").split(",")[0],S=B.effect.indexOf(",")<0?L:B.effect.replace(" ","").split(",")[1],O=0,N=0,C=0,P=0,U,H,I,X,W,T,K,F;function E(c,b,a){if(!H&&U){H=true;B.animationStart(P+1);switch(c){case"next":N=P;O=P+1;O=Z===O?0:O;X=Q*2;c=-Q*2;P=O;break;case"prev":N=P;O=P-1;O=O===-1?Z-1:O;X=0;c=0;P=O;break;case"pagination":O=parseInt(a,10);N=A("."+B.paginationClass+" li."+B.currentClass+" a",V).attr("href").match("[^#/]+$");if(O>N){X=Q*2;c=-Q*2;}else{X=0;c=0;}P=O;break;}if(b==="fade"){if(B.crossfade){J.children(":eq("+O+")",V).css({zIndex:10}).fadeIn(B.fadeSpeed,B.fadeEasing,function(){if(B.autoHeight){J.animate({height:J.children(":eq("+O+")",V).outerHeight()},B.autoHeightSpeed,function(){J.children(":eq("+N+")",V).css({display:"none",zIndex:0});J.children(":eq("+O+")",V).css({zIndex:0});B.animationComplete(O+1);H=false;});}else{J.children(":eq("+N+")",V).css({display:"none",zIndex:0});J.children(":eq("+O+")",V).css({zIndex:0});B.animationComplete(O+1);H=false;}});}else{J.children(":eq("+N+")",V).fadeOut(B.fadeSpeed,B.fadeEasing,function(){if(B.autoHeight){J.animate({height:J.children(":eq("+O+")",V).outerHeight()},B.autoHeightSpeed,function(){J.children(":eq("+O+")",V).fadeIn(B.fadeSpeed,B.fadeEasing);});}else{J.children(":eq("+O+")",V).fadeIn(B.fadeSpeed,B.fadeEasing,function(){if(A.browser.msie){A(this).get(0).style.removeAttribute("filter");}});}B.animationComplete(O+1);H=false;});}}else{J.children(":eq("+O+")").css({left:X,display:"block"});if(B.autoHeight){J.animate({left:c,height:J.children(":eq("+O+")").outerHeight()},B.slideSpeed,B.slideEasing,function(){J.css({left:-Q});J.children(":eq("+O+")").css({left:Q,zIndex:5});J.children(":eq("+N+")").css({left:Q,display:"none",zIndex:0});B.animationComplete(O+1);H=false;});}else{J.animate({left:c},B.slideSpeed,B.slideEasing,function(){J.css({left:-Q});J.children(":eq("+O+")").css({left:Q,zIndex:5});J.children(":eq("+N+")").css({left:Q,display:"none",zIndex:0});B.animationComplete(O+1);H=false;});}}if(B.pagination){A("."+B.paginationClass+" li."+B.currentClass,V).removeClass(B.currentClass);A("."+B.paginationClass+" li:eq("+O+")",V).addClass(B.currentClass);}}}function R(){clearInterval(V.data("interval"));}function G(){if(B.pause){clearTimeout(V.data("pause"));clearInterval(V.data("interval"));K=setTimeout(function(){clearTimeout(V.data("pause"));F=setInterval(function(){E("next",L);},B.play);V.data("interval",F);},B.pause);V.data("pause",K);}else{R();}}if(Z<2){return ;}if(D<0){D=0;}if(D>Z){D=Z-1;}if(B.start){P=D;}if(B.randomize){J.randomize();}A("."+B.container,V).css({overflow:"hidden",position:"relative"});J.children().css({position:"absolute",top:0,left:J.children().outerWidth(),zIndex:0,display:"none"});J.css({position:"relative",width:(Q*3),height:M,left:-Q});A("."+B.container,V).css({display:"block"});if(B.autoHeight){J.children().css({height:"auto"});J.animate({height:J.children(":eq("+D+")").outerHeight()},B.autoHeightSpeed);}if(B.preload&&J.find("img:eq("+D+")").length){A("."+B.container,V).css({background:"url("+B.preloadImage+") no-repeat 50% 50%"});var Y=J.find("img:eq("+D+")").attr("src")+"?"+(new Date()).getTime();if(A("img",V).parent().attr("class")!="slides_control"){T=J.children(":eq(0)")[0].tagName.toLowerCase();}else{T=J.find("img:eq("+D+")");}J.find("img:eq("+D+")").attr("src",Y).load(function(){J.find(T+":eq("+D+")").fadeIn(B.fadeSpeed,B.fadeEasing,function(){A(this).css({zIndex:5});A("."+B.container,V).css({background:""});U=true;B.slidesLoaded();});});}else{J.children(":eq("+D+")").fadeIn(B.fadeSpeed,B.fadeEasing,function(){U=true;B.slidesLoaded();});}if(B.bigTarget){J.children().css({cursor:"pointer"});J.children().click(function(){E("next",L);return false;});}if(B.hoverPause&&B.play){J.bind("mouseover",function(){R();});J.bind("mouseleave",function(){G();});}if(B.generateNextPrev){A("."+B.container,V).after('<a href="#" class="'+B.prev+'">Prev</a>');A("."+B.prev,V).after('<a href="#" class="'+B.next+'">Next</a>');}A("."+B.next,V).click(function(a){a.preventDefault();if(B.play){G();}E("next",L);});A("."+B.prev,V).click(function(a){a.preventDefault();if(B.play){G();}E("prev",L);});if(B.generatePagination){if(B.prependPagination){V.prepend("<ul class="+B.paginationClass+"></ul>");}else{V.append("<ul class="+B.paginationClass+"></ul>");}J.children().each(function(){A("."+B.paginationClass,V).append('<li><a href="#'+C+'">'+(C+1)+"</a></li>");C++;});}else{A("."+B.paginationClass+" li a",V).each(function(){A(this).attr("href","#"+C);C++;});}A("."+B.paginationClass+" li:eq("+D+")",V).addClass(B.currentClass);A("."+B.paginationClass+" li a",V).click(function(){if(B.play){G();}I=A(this).attr("href").match("[^#/]+$");if(P!=I){E("pagination",S,I);}return false;});A("a.link",V).click(function(){if(B.play){G();}I=A(this).attr("href").match("[^#/]+$")-1;if(P!=I){E("pagination",S,I);}return false;});if(B.play){F=setInterval(function(){E("next",L);},B.play);V.data("interval",F);}});};A.fn.slides.option={preload:false,preloadImage:"/img/loading.gif",container:"slides_container",generateNextPrev:false,next:"next",prev:"prev",pagination:true,generatePagination:true,prependPagination:false,paginationClass:"pagination",currentClass:"current",fadeSpeed:350,fadeEasing:"",slideSpeed:350,slideEasing:"",start:1,effect:"slide",crossfade:false,randomize:false,play:0,pause:0,hoverPause:false,autoHeight:false,autoHeightSpeed:350,bigTarget:false,animationStart:function(){},animationComplete:function(){},slidesLoaded:function(){}};A.fn.randomize=function(C){function B(){return(Math.round(Math.random())-0.5);}return(A(this).each(function(){var F=A(this);var E=F.children();var D=E.length;if(D>1){E.hide();var G=[];for(i=0;i<D;i++){G[G.length]=i;}G=G.sort(B);A.each(G,function(I,H){var K=E.eq(H);var J=K.clone(true);J.show().appendTo(F);if(C!==undefined){C(K,J);}K.remove();});}}));};})(jQuery);
-
left:0px;
+
-
}
+
-
/* If an image is wrapped in a link */
+
-
.nivoSlider a.nivo-imageLink {
+
-
position:absolute;
+
-
top:0px;
+
-
left:0px;
+
-
width:100%;
+
-
height:100%;
+
-
border:0;
+
-
padding:0;
+
-
margin:0;
+
-
z-index:6;
+
-
display:none;
+
-
}
+
-
/* The slices and boxes in the Slider */
+
-
.nivo-slice {
+
-
display:block;
+
-
position:absolute;
+
-
z-index:5;
+
-
height:100%;
+
-
}
+
-
.nivo-box {
+
-
display:block;
+
-
position:absolute;
+
-
z-index:5;
+
-
}
+
-
/* Caption styles */
+
-
.nivo-caption {
+
-
position:absolute;
+
-
left:0px;
+
-
bottom:0px;
+
-
background:#000;
+
-
color:#fff;
+
-
opacity:0.8; /* Overridden by captionOpacity setting */
+
-
width:100%;
+
-
z-index:8;
+
-
}
+
-
.nivo-caption p {
+
-
padding:5px;
+
-
margin:0;
+
-
}
+
-
.nivo-caption a {
+
-
display:inline !important;
+
-
}
+
-
.nivo-html-caption {
+
-
    display:none;
+
-
}
+
-
/* Direction nav styles (e.g. Next & Prev) */
+
-
.nivo-directionNav a {
+
-
position:absolute;
+
-
top:45%;
+
-
z-index:9;
+
-
cursor:pointer;
+
-
}
+
-
.nivo-prevNav {
+
-
left:15px;
+
-
}
+
-
.nivo-nextNav {
+
-
right:15px;
+
-
}
+
-
/* Control nav styles (e.g. 1,2,3...) */
+
-
.theme-default .nivo-controlNav {
+
-
      position:absolute; left:100%; bottom:-42px;
+
-
      margin-left: -1000px;
+
-
}
+
-
 
+
-
.nivo-controlNav a {
+
-
position:relative;
+
-
z-index:9;
+
-
cursor:pointer;
+
-
}
+
-
 
+
-
 
+
-
 
+
-
.nivo-controlNav a.active {
+
-
font-weight:bold;
+
-
}
+
-
 
+
-
.theme-default #slider {
+
-
    margin:0px auto 0px auto;
+
-
    width:618px; /* Make sure your images are the same size */
+
-
    height:464px; /* Make sure your images are the same size */
+
-
}
+
-
 
+
-
 
+
-
 
+
-
</style>
+
 +
</script>
</html>
</html>

Revision as of 17:58, 18 June 2013


Our project focuses on promoter engineering. Our goal is to characterize a set of promoters (of our design) by moving the repressor and/or activator binding sites with respect to the -10 and -35 regions of the promoter. Ideally, we would like to show that by moving an activator binding site it can become a repressor and that by moving a repressor binding site it may become either irrelevant to transcription rate or even boost it. We also want to see if there is a steep decline in repressor/activator function as the binding site move along the promoter or if it is a gradual/linear change. We believe this project could have application to genetic circuits by allowing a single protein to either activate or repress a promoter depending on where the binding sites are placed on the promoter.