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| - | <html>
| |
| - | <head>
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| - | <title>Edinburgh iGEM 2008</title>
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| - | <script type="text/javascript">
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| - | //Drop Down Tabs Menu- Author: Dynamic Drive (http://www.dynamicdrive.com)
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| - | //Created: May 16th, 07'
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| | | | |
| - | var tabdropdown={
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| - | disappeardelay: 200, //set delay in miliseconds before menu disappears onmouseout
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| - | disablemenuclick: false, //when user clicks on a menu item with a drop down menu, disable menu item's link?
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| - | enableiframeshim: 1, //1 or 0, for true or false
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| - |
| |
| - | //No need to edit beyond here////////////////////////
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| - | dropmenuobj: null, ie: document.all, firefox: document.getElementById&&!document.all, previousmenuitem:null
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| - | currentpageurl: window.location.href.replace("http://"+window.location.hostname, "").replace(/^\//, ""), //get current page url (minus hostname, ie: http://www.dynamicdrive.com/)
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| - |
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| - | getposOffset:function(what, offsettype){
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| - | var totaloffset=(offsettype=="left")? what.offsetLeft : what.offsetTop;
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| - | var parentEl=what.offsetParent;
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| - | while (parentEl!=null){
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| - | totaloffset=(offsettype=="left")? totaloffset+parentEl.offsetLeft : totaloffset+parentEl.offsetTop;
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| - | parentEl=parentEl.offsetParent;
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| - | }
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| - | return totaloffset;
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| - | },
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| - |
| |
| - | showhide:function(obj, e, obj2){ //obj refers to drop down menu, obj2 refers to tab menu item mouse is currently over
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| - | if (this.ie || this.firefox)
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| - | this.dropmenuobj.style.left=this.dropmenuobj.style.top="-500px"
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| - | if (e.type=="click" && obj.visibility==hidden || e.type=="mouseover"){
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| - | if (obj2.parentNode.className.indexOf("default")==-1) //if tab isn't a default selected one
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| - | obj2.parentNode.className="selected"
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| - | obj.visibility="visible"
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| - | }
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| - | else if (e.type=="click")
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| - | obj.visibility="hidden"
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| - | },
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| - |
| |
| - | iecompattest:function(){
| |
| - | return (document.compatMode && document.compatMode!="BackCompat")? document.documentElement : document.body
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| - | },
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| - |
| |
| - | clearbrowseredge:function(obj, whichedge){
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| - | var edgeoffset=0
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| - | if (whichedge=="rightedge"){
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| - | var windowedge=this.ie && !window.opera? this.standardbody.scrollLeft+this.standardbody.clientWidth-15 : window.pageXOffset+window.innerWidth-15
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| - | this.dropmenuobj.contentmeasure=this.dropmenuobj.offsetWidth
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| - | if (windowedge-this.dropmenuobj.x < this.dropmenuobj.contentmeasure) //move menu to the left?
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| - | edgeoffset=this.dropmenuobj.contentmeasure-obj.offsetWidth
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| - | }
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| - | else{
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| - | var topedge=this.ie && !window.opera? this.standardbody.scrollTop : window.pageYOffset
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| - | var windowedge=this.ie && !window.opera? this.standardbody.scrollTop+this.standardbody.clientHeight-15 : window.pageYOffset+window.innerHeight-18
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| - | this.dropmenuobj.contentmeasure=this.dropmenuobj.offsetHeight
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| - | if (windowedge-this.dropmenuobj.y < this.dropmenuobj.contentmeasure){ //move up?
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| - | edgeoffset=this.dropmenuobj.contentmeasure+obj.offsetHeight
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| - | if ((this.dropmenuobj.y-topedge)<this.dropmenuobj.contentmeasure) //up no good either?
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| - | edgeoffset=this.dropmenuobj.y+obj.offsetHeight-topedge
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| - | }
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| - | this.dropmenuobj.firstlink.style.borderTopWidth=(edgeoffset==0)? 0 : "1px" //Add 1px top border to menu if dropping up
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| - | }
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| - | return edgeoffset
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| - | },
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| - |
| |
| - | dropit:function(obj, e, dropmenuID){
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| - | if (this.dropmenuobj!=null){ //hide previous menu
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| - | this.dropmenuobj.style.visibility="hidden" //hide menu
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| - | if (this.previousmenuitem!=null && this.previousmenuitem!=obj){
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| - | if (this.previousmenuitem.parentNode.className.indexOf("default")==-1) //If the tab isn't a default selected one
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| - | this.previousmenuitem.parentNode.className=""
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| - | }
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| - | }
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| - | this.clearhidemenu()
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| - | if (this.ie||this.firefox){
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| - | obj.onmouseout=function(){tabdropdown.delayhidemenu(obj)}
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| - | obj.onclick=function(){return !tabdropdown.disablemenuclick} //disable main menu item link onclick?
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| - | this.dropmenuobj=document.getElementById(dropmenuID)
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| - | this.dropmenuobj.onmouseover=function(){tabdropdown.clearhidemenu()}
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| - | this.dropmenuobj.onmouseout=function(e){tabdropdown.dynamichide(e, obj)}
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| - | this.dropmenuobj.onclick=function(){tabdropdown.delayhidemenu(obj)}
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| - | this.showhide(this.dropmenuobj.style, e, obj)
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| - | this.dropmenuobj.x=this.getposOffset(obj, "left")
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| - | this.dropmenuobj.y=this.getposOffset(obj, "top")
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| - | this.dropmenuobj.style.left=this.dropmenuobj.x-this.clearbrowseredge(obj, "rightedge")+"px"
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| - | this.dropmenuobj.style.top=this.dropmenuobj.y-this.clearbrowseredge(obj, "bottomedge")+obj.offsetHeight+1+"px"
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| - | this.previousmenuitem=obj //remember main menu item mouse moved out from (and into current menu item)
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| - | this.positionshim() //call iframe shim function
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| - | }
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| - | },
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| - |
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| - | contains_firefox:function(a, b) {
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| - | while (b.parentNode)
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| - | if ((b = b.parentNode) == a)
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| - | return true;
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| - | return false;
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| - | },
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| - |
| |
| - | dynamichide:function(e, obj2){ //obj2 refers to tab menu item mouse is currently over
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| - | var evtobj=window.event? window.event : e
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| - | if (this.ie&&!this.dropmenuobj.contains(evtobj.toElement))
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| - | this.delayhidemenu(obj2)
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| - | else if (this.firefox&&e.currentTarget!= evtobj.relatedTarget&& !this.contains_firefox(evtobj.currentTarget, evtobj.relatedTarget))
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| - | this.delayhidemenu(obj2)
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| - | },
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| - |
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| - | delayhidemenu:function(obj2){
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| - | this.delayhide=setTimeout(function(){tabdropdown.dropmenuobj.style.visibility='hidden'; if (obj2.parentNode.className.indexOf('default')==-1) obj2.parentNode.className=''},this.disappeardelay) //hide menu
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| - | },
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| - |
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| - | clearhidemenu:function(){
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| - | if (this.delayhide!="undefined")
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| - | clearTimeout(this.delayhide)
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| - | },
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| - |
| |
| - | positionshim:function(){ //display iframe shim function
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| - | if (this.enableiframeshim && typeof this.shimobject!="undefined"){
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| - | if (this.dropmenuobj.style.visibility=="visible"){
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| - | this.shimobject.style.width=this.dropmenuobj.offsetWidth+"px"
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| - | this.shimobject.style.height=this.dropmenuobj.offsetHeight+"px"
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| - | this.shimobject.style.left=this.dropmenuobj.style.left
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| - | this.shimobject.style.top=this.dropmenuobj.style.top
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| - | }
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| - | this.shimobject.style.display=(this.dropmenuobj.style.visibility=="visible")? "block" : "none"
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| - | }
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| - | },
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| - |
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| - | hideshim:function(){
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| - | if (this.enableiframeshim && typeof this.shimobject!="undefined")
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| - | this.shimobject.style.display='none'
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| - | },
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| - |
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| - | isSelected:function(menuurl){
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| - | var menuurl=menuurl.replace("http://"+menuurl.hostname, "").replace(/^\//, "")
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| - | return (tabdropdown.currentpageurl==menuurl)
| |
| - | },
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| - |
| |
| - | init:function(menuid, dselected){
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| - | this.standardbody=(document.compatMode=="CSS1Compat")? document.documentElement : document.body //create reference to common "body" across doctypes
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| - | var menuitems=document.getElementById(menuid).getElementsByTagName("a")
| |
| - | for (var i=0; i<menuitems.length; i++){
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| - | if (menuitems[i].getAttribute("rel")){
| |
| - | var relvalue=menuitems[i].getAttribute("rel")
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| - | document.getElementById(relvalue).firstlink=document.getElementById(relvalue).getElementsByTagName("a")[0]
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| - | menuitems[i].onmouseover=function(e){
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| - | var event=typeof e!="undefined"? e : window.event
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| - | tabdropdown.dropit(this, event, this.getAttribute("rel"))
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| - | }
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| - | }
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| - | if (dselected=="auto" && typeof setalready=="undefined" && this.isSelected(menuitems[i].href)){
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| - | menuitems[i].parentNode.className+=" selected default"
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| - | var setalready=true
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| - | }
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| - | else if (parseInt(dselected)==i)
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| - | menuitems[i].parentNode.className+=" selected default"
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| - | }
| |
| - | }
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| - |
| |
| - | }
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| - | </script>
| |
| - | <style>
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| - | .ddcolortabs{
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| - | padding: 0;
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| - | width: 100%;
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| - | background: transparent;
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| - | voice-family: "\"}\"";
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| - | voice-family: inherit;
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| - | }
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| - |
| |
| - | .ddcolortabs ul{
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| - | font: normal 11px Arial, Verdana, sans-serif;
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| - | margin:0;
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| - | padding:0;
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| - | list-style:none;
| |
| - | }
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| - |
| |
| - | .ddcolortabs li{
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| - | display:inline;
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| - | margin:0 2px 0 0;
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| - | padding:0;
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| - | text-transform:uppercase;
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| - | }
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| - |
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| - |
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| - | .ddcolortabs a{
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| - | float:left;
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| - | color: white;
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| - | background: black url(media/color_tabs_left.gif) no-repeat left top;
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| - | margin:0 2px 0 0;
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| - | padding:0 0 1px 3px;
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| - | text-decoration:none;
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| - | letter-spacing: 1px;
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| - | }
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| - |
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| - | .ddcolortabs a span{
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| - | float:left;
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| - | display:block;
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| - | background: transparent url(media/color_tabs_right.gif) no-repeat right top;
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| - | padding: 4px 8px 2px 7px;
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| - | }
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| - |
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| - | .ddcolortabs a span{
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| - | float:none;
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| - | }
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| - |
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| - | .ddcolortabs a:hover{
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| - | background-color: #591f20;
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| - | }
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| - |
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| - | .ddcolortabs a:hover span{
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| - | background-color: #591f20;
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| - | }
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| - |
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| - | .ddcolortabs .selected a, #ddcolortabs .selected a span{ /*currently selected tab*/
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| - | background-color: #591f20;
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| - | }
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| - |
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| - | .ddcolortabsline{
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| - | clear: both;
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| - | padding: 0;
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| - | width: 100%;
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| - | height: 8px;
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| - | line-height: 8px;
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| - | background: black;
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| - | border-top: 1px solid #fff; /*Remove this to remove border between bar and tabs*/
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| - | }
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| - |
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| - | /* ######### Style for Drop Down Menu ######### */
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| - |
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| - | .dropmenudiv_a{
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| - | position:absolute;
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| - | top: 0;
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| - | border: 1px solid black; /*THEME CHANGE HERE*/
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| - | border-top-width: 8px; /*Top border width. Should match height of .ddcolortabsline above*/
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| - | border-bottom-width: 0;
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| - | font:normal 12px Arial;
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| - | line-height:18px;
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| - | z-index:100;
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| - | background-color: white;
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| - | width: 200px;
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| - | visibility: hidden;
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| - | }
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| - |
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| - |
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| - | .dropmenudiv_a a{
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| - | width: auto;
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| - | display: block;
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| - | text-indent: 5px;
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| - | border-top: 0 solid #678b3f;
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| - | border-bottom: 1px solid #678b3f; /*THEME CHANGE HERE*/
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| - | padding: 2px 0;
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| - | text-decoration: none;
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| - | color: black;
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| - | }
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| - |
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| - | * html .dropmenudiv_a a{ /*IE only hack*/
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| - | width: 100%;
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| - | }
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| - |
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| - | .dropmenudiv_a a:hover{ /*THEME CHANGE HERE*/
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| - | background-color: #8a3c3d;
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| - | color: white;
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| - | }
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| - | </style>
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| - | </head>
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| - |
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| - | <!-- CSS for Drop Down Tabs Menu #1 -->
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| - | <link rel="stylesheet" type="text/css" href="ddcolortabs.css" />
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| - |
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| - | <div id="colortab" class="ddcolortabs">
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| - | <ul>
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| - | <li><a href="https://2008.igem.org/Team:Edinburgh" title="Home"><span>Home</span></a></li>
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| - | <li><a href="https://2008.igem.org/Team:Edinburgh/Project" title="Project" rel="dropmenu1_a"><span>The Project</span></a></li>
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| - | <li><a href="https://2008.igem.org/Team:Edinburgh/Team" title="Team" ><span>The Team</span></a></li>
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| - | <li><a href="https://2008.igem.org/Team:Edinburgh/Modeling" title="Modeling" rel="dropmenu2_a"><span>Modeling</span></a></li>
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| - | <li><a href="https://2008.igem.org/Team:Edinburgh/Notebook" title="Notebook"><span>Notebook</span></a></li>
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| - | </ul>
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| - | </div>
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| - | <div class="ddcolortabsline"> </div>
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| - | <div id="dropmenu1_a" class="dropmenudiv_a">
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| - | <a href="https://2008.igem.org/Team:Edinburgh/Team">Overview</a>
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| - | <a href="https://2008.igem.org/Team:Edinburgh/Team">Step1</a>
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| - | <a href="https://2008.igem.org/Team:Edinburgh/Team">Step2</a>
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| - | </div>
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| - | <script type="text/javascript">
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| - | //SYNTAX: tabdropdown.init("menu_id", [integer OR "auto"])
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| - | tabdropdown.init("colortab", 3)
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| - | </script>
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| - | </html>
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| - |
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| - | For more information, please see [https://www.wiki.ed.ac.uk/display/iGEM2008/HOME our internal wiki].
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| - |
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| - | ==Our Objective: Saving the World==
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| - |
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| - | "Cellulose is the most abundant form of fixed carbon, with 100,000,000,000 tons produced in cell walls by plants each year" [http://www.blackwell-synergy.com/doi/full/10.1196/annals.1419.026 (Wilson, 2008)].
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| - |
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| - | A food shortage is engulfing the entire world, pushing food prices to new highs. An essay from the [http://www.earthpolicy.org/Updates/2008/Update72.htm Earth Policy Institute] (16 April 2008) discusses its significance to our lives. The food shortage not only harms the economy but also overburdens the environment, putting the future of the human race in peril. Coupled to this is global warming resulting in more frequent and lengthier periods of drought for much of the world as well as predicted inundation of low-lying land, and the depletion of oil reserves, which together but further strain on ecosystems.
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| - |
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| - | ==Project Description: Engineering bacteria to convert cellulose into starch and to produce the vitamin A precursor, beta-carotene==
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| - |
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| - | Currently, much agricultural produce is wasted. Wouldn't it be great if the indigestible parts of crop plants could be made edible, or at least if they could be converted into a biofuel source? - This is our plan!
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| - |
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| - | We will engineer bacteria with three novel pathways:
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| - | # Degrade cellulose into glucose
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| - | # Synthesise starch from glucose
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| - | # Synthesise beta-carotene from glucose
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| - |
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| - | [[Image:Edinburgh_Flowchart.jpg|200px]]
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| - | Click the thumbnail for an overview flowchart.
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| - |
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| - | ===1. Cellulose degradation===
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| - |
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| - | We plan to incorporate the ''Cellulomonas fimi'' endoglucanase genes ''cenA'', ''cenB'' and ''cenC'', exoglucanase gene ''cex'' and beta-glucosidase into bacteria. Together these genes will be capable of breaking down cellulose into glucose. The proteins will need to be secreted into the medium to act (cellulose being too large for uptake into the cells), and we have 3 plans to enable this:
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| - | # Add the Hly secretory pathway into a lab strain of ''E. coli'' (K12, JM109). This will involve incorporating ''hlyB'', ''hlyD'' and ''tolC'' and adding the 3' end of ''hlyA'' to our cellulases.
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| - | # Create a glucose-sensitive feedback mechanism of cell lysis. Depletion of glucose would cause transcription of our cellulase operon and the transcription factor ''comK''. ComK would bind to a promoter upstream of the phiX174 gene ''E''. E is a short peptide which causes cell lysis.
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| - | # Engineer our genes into ''Bacillus subtilis'', in which secretion is much better understand than in ''E. coli''.
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| - |
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| - | ===2. Starch synthesis===
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| - |
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| - | The first phase in synthesising starch make use of the chasis' native glycogen synthesis pathway. The gene ''glgC'' (ADP-glucose pyrophosphorylase, catalysing the convertion glucose 1-phosphate and ATP to ADP-glucose and PPi) is responsible for the most rate-limiting step of glycogen synthesis in ''E. coli''. This is because the protein is negatively regulated by PPi. Carrying out the substitution 336:Gly->Asp to ''glgC'' has been reported to increase the yield of glycogen due to the loss allosteric inhibition. This mutated form of ''glgC'' is one of the BioBricks which we are in the process of making.
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| - |
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| - | The second phase is the conversion of glycogen to starch. To achieve this we are creating isoamylase and granule-bound starch synthesase BioBricks (''isa1'', ''isa2'' and ''gbss'') from ''Zea mays'' cDNAs. These three genes together should be sufficient for the production of starch from glycogen.
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| - |
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| - | ===3. Beta-carotene synthesis===
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| - |
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| - | Vitamin A deficiency results in night-blindness and an impaired immune system. A number of genes from ''Pantoea ananatis'' will be added to our bacterial cells, in essence transferring the beta-carotene synthesis pathway of ''P. ananatis'' to our chasis organism. These genes are ''crtE'' (geranyl diphosphate synthesase), ''crtB'' (phytoene synthase), ''crtI'' (phytoene desaturase) and ''crtY'' (lycopene beta-cyclase). We will also create BioBricks of the ''E. coli'' genes ''dxs'' and ''appY'', the addition of which should increase the yield of beta-carotene.
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| - |
| |
| - | ==Flowchart==
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| - |
| |
| - | [[Image:Edinburgh_Flowchart.jpg|500px]]
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| - |
| |
| - | ==Calendar==
| |
| - | [[Image:Calendar.jpg]]
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"
