Edinburgh/18 July 2008

From 2008.igem.org

(Difference between revisions)
(New page: <html> <head> <title>Edinburgh iGEM 2008</title> <script type="text/javascript"> //Drop Down Tabs Menu- Author: Dynamic Drive (http://www.dynamicdrive.com) //Created: May 16th, 07' var ta...)
 
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<html>
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<div id="header">{{Template:Team:Edinburgh/Templates/notebook-entry/header}}</div>
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<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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:::: '''[[Edinburgh/17_July_2008|< Previous Entry]]'''
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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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== Week 5 ==
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dropmenuobj: null, ie: document.all, firefox: document.getElementById&&!document.all, previousmenuitem:null,
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=== Friday 18 July 08 ===
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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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getposOffset:function(what, offsettype){
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* Made pSB1A2+''appY'' maxiprep '''X3'''. (AM)
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var totaloffset=(offsettype=="left")? what.offsetLeft : what.offsetTop;
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* Purified PCR products for ''cenA'', ''cenB'', ''cenC'' and ''cex'' (P16 to P19) run on '''Gel 16'''. No visible bands. (AM)
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var parentEl=what.offsetParent;
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* Second attempt at PCR for ''cenA'', ''cenB'', ''cenC'' and ''cex'' ('''P20''' to '''P23'''). Annealing 55°C, extension 85s; did ''not'' include glycerol. Ran unpurified PCR products on '''Gel 17''' - no bands apart from thick bands in the <0.5kb region = primers. Hence, PCR was unsuccessful. (AM)
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while (parentEl!=null){
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* Transformed L16 (pSB1A2+rbs+''appY''), '''plates 46 and 47'''.<br />
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totaloffset=(offsettype=="left")? totaloffset+parentEl.offsetLeft : totaloffset+parentEl.offsetTop;
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<br />
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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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:::: '''[[Edinburgh/19_July_2008|Next Entry >]]'''
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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(){
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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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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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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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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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+
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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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},
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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")
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for (var i=0; i<menuitems.length; i++){
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if (menuitems[i].getAttribute("rel")){
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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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+
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}
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</script>
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<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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-
}
+
-
 
+
-
.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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}
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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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.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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.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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.ddcolortabs a:hover{
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background-color: #591f20;
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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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.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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.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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/* ######### Style for Drop Down Menu ######### */
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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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.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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* html .dropmenudiv_a a{ /*IE only hack*/
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-
width: 100%;
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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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<!-- CSS for Drop Down Tabs Menu #1 -->
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<link rel="stylesheet" type="text/css" href="ddcolortabs.css" />
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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="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=Edinburgh" title="Project" rel="dropmenu1_a"><span>BioBrick Parts</span></a></li>
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<li><a href="https://2008.igem.org/Team:Edinburgh/Modeling" title="Modelling" rel="dropmenu2_a"><span>Modelling</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">&nbsp;</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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=== Week 5 ===
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==== Thursday 17 July 08 ====
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* PCR for ''cenA'', ''cenB'', ''cenC'' and ''cex'' ('''P16''', '''P17''', '''P18''', '''P19'''). Annealing 58°C, extension 115s (''cenB'' and ''cenC'' are both over 3kb) and included 5% v/v glycerol in the reactions since in the past that has been helpful with high GC templates. PCR products purified to be run on gel tomorrow (against wisdom, since they should have been run on gel both before and after purification).
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* Results of transformations: plenty of colonies for ''glgC'' mutation (mutating site 1 in the mutant which already has site 2 mutated). Subbed some of these to '''plates 42, 44 and 45''' (poor communications). Only a few colonies for rbs+''dxs'', and only one of these was white. Subbed this to '''plate 43'''. Apparently there may have been some problem with the purification of this digest - may need to repeat.
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* Re-digested M32, M36 (''pSB1A2-crtB''), M39 and M40 (''pSB1A2-crtI'') and ran on '''Gel 15'''. Gel unsuccessful - stain smeared over 0.5-2kb region, exactly where ''crtB'' and ''crtI'' bands are expected to appear. Perhaps too much loading buffer or problem with the tank (tank with 'loose wire' was used). (AM)
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* pSB1A2+''appY'' cultures set up in beaker for maxiprep tomorrow ('''X3'''). (AM)
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Latest revision as of 14:09, 28 August 2008

< Previous Entry

Week 5

Friday 18 July 08

  • Made pSB1A2+appY maxiprep X3. (AM)
  • Purified PCR products for cenA, cenB, cenC and cex (P16 to P19) run on Gel 16. No visible bands. (AM)
  • Second attempt at PCR for cenA, cenB, cenC and cex (P20 to P23). Annealing 55°C, extension 85s; did not include glycerol. Ran unpurified PCR products on Gel 17 - no bands apart from thick bands in the <0.5kb region = primers. Hence, PCR was unsuccessful. (AM)
  • Transformed L16 (pSB1A2+rbs+appY), plates 46 and 47.


Next Entry >
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