Edinburgh/30 June 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/29_June_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 3 ==
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dropmenuobj: null, ie: document.all, firefox: document.getElementById&&!document.all, previousmenuitem:null,
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=== Monday 30 June 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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* Plasmid DNA minipreps:
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var totaloffset=(offsettype=="left")? what.offsetLeft : what.offsetTop;
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** '''M1 to M6''': pSB1A2+''dxs'' white colonies from plate 11
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var parentEl=what.offsetParent;
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** '''M7''': BABEL1+''glgC'' white colony from plate 12
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while (parentEl!=null){
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** '''M8 to M12''': BABEL2+''glgC'' white and pale blue colonies from plate 13
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totaloffset=(offsettype=="left")? totaloffset+parentEl.offsetLeft : totaloffset+parentEl.offsetTop;
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* M1 to M6 were digested with EcoRI/PstI ('''Gel 2'''). The expected pattern is pSB1A2 vector band at 2.04kb (2079 bp less prefix and suffix) and ''dxs'' insert band around 1.9kb. M1 showed bands around 1.1kb and 2.1kb. M5 showed no DNA. The other four showed a vector-like band around 2kb and a fainter, fuzzier band around 3kb, possibly a 'ghost' band. Thus none of the clones show the expected pattern of bands (although it is conceivable, since the vector and insert bands are so close in size, that they may be lying on top of each other; ''dxs'' has an internal EcoRV site at +504 and two HindIII sites at +606 and +1230, whereas pSB1A2 lacks such sites so this could be used to check). In conjunction with the total lack of growth on the ''appY'' plates, this suggests that something went wrong in the cloning procedure. The next step is to run the remaining ligation material on a gel and see what it looks like.<br />
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parentEl=parentEl.offsetParent;
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<br />
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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/1_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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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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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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+
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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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clearhidemenu:function(){
+
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if (this.delayhide!="undefined")
+
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clearTimeout(this.delayhide)
+
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},
+
-
 
+
-
positionshim:function(){ //display iframe shim function
+
-
if (this.enableiframeshim && typeof this.shimobject!="undefined"){
+
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if (this.dropmenuobj.style.visibility=="visible"){
+
-
this.shimobject.style.width=this.dropmenuobj.offsetWidth+"px"
+
-
this.shimobject.style.height=this.dropmenuobj.offsetHeight+"px"
+
-
this.shimobject.style.left=this.dropmenuobj.style.left
+
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this.shimobject.style.top=this.dropmenuobj.style.top
+
-
}
+
-
this.shimobject.style.display=(this.dropmenuobj.style.visibility=="visible")? "block" : "none"
+
-
}
+
-
},
+
-
 
+
-
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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isSelected:function(menuurl){
+
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var menuurl=menuurl.replace("http://"+menuurl.hostname, "").replace(/^\//, "")
+
-
return (tabdropdown.currentpageurl==menuurl)
+
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},
+
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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")
+
-
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]
+
-
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"))
+
-
}
+
-
}
+
-
if (dselected=="auto" && typeof setalready=="undefined" && this.isSelected(menuitems[i].href)){
+
-
menuitems[i].parentNode.className+=" selected default"
+
-
var setalready=true
+
-
}
+
-
else if (parseInt(dselected)==i)
+
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menuitems[i].parentNode.className+=" selected default"
+
-
}
+
-
}
+
-
 
+
-
}
+
-
</script>
+
-
<style>
+
-
.ddcolortabs{
+
-
padding: 0;
+
-
width: 100%;
+
-
background: transparent;
+
-
voice-family: "\"}\"";
+
-
voice-family: inherit;
+
-
}
+
-
 
+
-
.ddcolortabs ul{
+
-
font: normal 11px Arial, Verdana, sans-serif;
+
-
margin:0;
+
-
padding:0;
+
-
list-style:none;
+
-
}
+
-
 
+
-
.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;
+
-
}
+
-
 
+
-
.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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.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;
+
-
font:normal 12px Arial;
+
-
line-height:18px;
+
-
z-index:100;
+
-
background-color: white;
+
-
width: 200px;
+
-
visibility: hidden;
+
-
}
+
-
 
+
-
 
+
-
.dropmenudiv_a a{
+
-
width: auto;
+
-
display: block;
+
-
text-indent: 5px;
+
-
border-top: 0 solid #678b3f;
+
-
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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* 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*/
+
-
background-color: #8a3c3d;
+
-
color: white;
+
-
}
+
-
</style>
+
-
</head>
+
-
 
+
-
<!-- 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>
+
-
</ul>
+
-
</div>
+
-
<div class="ddcolortabsline">&nbsp;</div>
+
-
<div id="dropmenu1_a" class="dropmenudiv_a">
+
-
<a href="https://2008.igem.org/Team:Edinburgh/Team">Overview</a>
+
-
<a href="https://2008.igem.org/Team:Edinburgh/Team">Step1</a>
+
-
<a href="https://2008.igem.org/Team:Edinburgh/Team">Step2</a>
+
-
</div>
+
-
<script type="text/javascript">
+
-
//SYNTAX: tabdropdown.init("menu_id", [integer OR "auto"])
+
-
tabdropdown.init("colortab", 3)
+
-
</script>
+
-
</html>
+
-
 
+
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=== Week 3 ===
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==== Monday 30 June 08 ====
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* Plasmid DNA minipreps:<br />
+
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'''M1 to M6:''' pSB1A2+''dxs'' white colonies<br />
+
-
'''M7:''' Babel1+''glgC'' white colony<br />
+
-
'''M8 to M12:''' Babel2+''glgC'' white and pale blue colonies<br />
+
-
Minipreps M1 to M6 were digested with EcoRI and PstI ('''Gel 2'''). The expected pattern is pSB1A2 vector band at 2.04kb (2079 bp less prefix and suffix) and ''dxs'' insert band around 1.9kb. M1 showed bands around 1.1kb and 2.1kb. M5 showed no DNA. The other four showed a vector-like band around 2kb and a fainter, fuzzier band around 3kb, possibly a 'ghost' band. Thus none of the clones show the expected pattern of bands (although it is conceivable, since the vector and insert bands are so close in size, that they may be lying on top of each other; ''dxs'' has an internal EcoRV site at +504 and two HindIII sites at +606 and +1230, whereas pSB1A2 lacks such sites so this could be used to check). In conjunction with the total lack of growth on the ''appY'' plates, this suggests that something went wrong in the cloning procedure. The next step is to run the remaining ligation material on a gel and see what it looks like.
+

Latest revision as of 14:04, 28 August 2008

< Previous Entry

Week 3

Monday 30 June 08

  • Plasmid DNA minipreps:
    • M1 to M6: pSB1A2+dxs white colonies from plate 11
    • M7: BABEL1+glgC white colony from plate 12
    • M8 to M12: BABEL2+glgC white and pale blue colonies from plate 13
  • M1 to M6 were digested with EcoRI/PstI (Gel 2). The expected pattern is pSB1A2 vector band at 2.04kb (2079 bp less prefix and suffix) and dxs insert band around 1.9kb. M1 showed bands around 1.1kb and 2.1kb. M5 showed no DNA. The other four showed a vector-like band around 2kb and a fainter, fuzzier band around 3kb, possibly a 'ghost' band. Thus none of the clones show the expected pattern of bands (although it is conceivable, since the vector and insert bands are so close in size, that they may be lying on top of each other; dxs has an internal EcoRV site at +504 and two HindIII sites at +606 and +1230, whereas pSB1A2 lacks such sites so this could be used to check). In conjunction with the total lack of growth on the appY plates, this suggests that something went wrong in the cloning procedure. The next step is to run the remaining ligation material on a gel and see what it looks like.


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