Edinburgh/12 August 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/11_August_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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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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parentEl=parentEl.offsetParent;
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return totaloffset;
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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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else if (e.type=="click")
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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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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.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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contains_firefox:function(a, b) {
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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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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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clearhidemenu:function(){
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if (this.delayhide!="undefined")
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clearTimeout(this.delayhide)
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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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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(/^\//, "")
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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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-
</script>
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<style>
+
-
.ddcolortabs{
+
-
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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-
 
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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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-
 
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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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-
 
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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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-
}
+
-
 
+
-
 
+
-
.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>
+
-
</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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-
 
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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>
+
-
<li><a href="https://2008.igem.org/Team:Edinburgh/Team" title="Team" ><span>The Team</span></a></li>
+
-
<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>
+
-
<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">
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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">
+
-
//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 9 ===
=== Week 9 ===
==== Tuesday 12 August 08 ====
==== Tuesday 12 August 08 ====
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* '''Plate 115''' made with subs from L33 (Pl. 109/110: pSB1A2+pCstA), L34 (Pl. 111/112: pSB1A2+''dxs''+''crtE'') and L35 (Pl. 113/114: pSB1A2+''dxs''+''lims1'') (CF)
+
* '''Plate 115''' made with subs from L33 (Pl. 109/110: pSB1A2+''P<sub>cstA</sub>''), L34 (Pl. 111/112: pSB1A2+''dxs''+''crtE'') and L35 (Pl. 113/114: pSB1A2+''dxs''+''lims1'') (CF)
-
* Over-night cultures of L33 (pSB1A2+pCstA, sub-cloned on Plate 115), L34 (pSB1A2+''dxs''+''crtE'', sub-cloned on Plate 115) and L35 (pSB1A2+''dxs''+''lims1'', subcloned on Plate 115) set up, ready for minipreps tomorrow.
+
* Over-night cultures of L33 (pSB1A2+''P<sub>cstA</sub>'', sub-cloned on Plate 115), L34 (pSB1A2+''dxs''+''crtE'', sub-cloned on Plate 115) and L35 (pSB1A2+''dxs''+''lims1'', subcloned on Plate 115) set up, ready for minipreps tomorrow.
* '''M121-M123''': Minipreps of pSB1A2+''crtY'' (1,2,3). '''M124-M126''': Minipreps of pSB1A2+rbs+''crtY'' (1,2,3). note: I messed up M121 by adding 200µl instead of 100µl of sol 1. They are in the green box, the orange one is full. (OG)
* '''M121-M123''': Minipreps of pSB1A2+''crtY'' (1,2,3). '''M124-M126''': Minipreps of pSB1A2+rbs+''crtY'' (1,2,3). note: I messed up M121 by adding 200µl instead of 100µl of sol 1. They are in the green box, the orange one is full. (OG)
* Double digests of M121 to M126, run on '''Gel 46'''. It looks good! M121 is good! (Yan)
* Double digests of M121 to M126, run on '''Gel 46'''. It looks good! M121 is good! (Yan)
Line 301: Line 15:
* Purified P57 (''cex'' from cell suspension) and P64 (''cex'' from genomic DNA). Digested both with PstI. (AM)
* Purified P57 (''cex'' from cell suspension) and P64 (''cex'' from genomic DNA). Digested both with PstI. (AM)
* PCR for ''cenA'' from ''C. fimi'' genomic DNA ('''P65'''): denaturing 1 min, annealing 56°C for 20s, extension 30s, with glycerol. (AM)
* PCR for ''cenA'' from ''C. fimi'' genomic DNA ('''P65'''): denaturing 1 min, annealing 56°C for 20s, extension 30s, with glycerol. (AM)
-
* P57 and P64 (''cex'') PstI digests and P65 (''cenA'') run on '''Gel 47'''. Results indicate success!. (AM)
+
* P57 and P64 (''cex'') PstI digests and P65 (''cenA'') run on '''Gel 47'''. Results indicate success! (AM)
* Re-did the excise of ''crtE'' from BABEL2 (M79); cut out the band responsible for ''crtE'' and Edinbrick 1 on the gel, followed by putification of ''crtE'' and Edinbrick1 from the cut-out gel. Finally, ligation of ''crtE'' to Edinbrick1 ('''L38'''). (HX, AH)
* Re-did the excise of ''crtE'' from BABEL2 (M79); cut out the band responsible for ''crtE'' and Edinbrick 1 on the gel, followed by putification of ''crtE'' and Edinbrick1 from the cut-out gel. Finally, ligation of ''crtE'' to Edinbrick1 ('''L38'''). (HX, AH)
* Analytical digests as follows (AH):
* Analytical digests as follows (AH):
Line 308: Line 22:
** M115 and M116 (pSB1A2+''glgC''-mut1,2): EcoRI/HindIII
** M115 and M116 (pSB1A2+''glgC''-mut1,2): EcoRI/HindIII
* Digests of M109, M110, M115 and M116 were run on '''gel 48'''. M109 and M110 should give two bands if both genes are present. HindIII digest of M115/116 should give a single band indicating linearised plasmid with ''glgC''. Double digest of M115/116 should give an insert band of ~1kb and a vector + ~500bp of insert band. Results do not look good. Bands seem to indicate much too large products, but will discuss with Chris tomorrow.(AH)
* Digests of M109, M110, M115 and M116 were run on '''gel 48'''. M109 and M110 should give two bands if both genes are present. HindIII digest of M115/116 should give a single band indicating linearised plasmid with ''glgC''. Double digest of M115/116 should give an insert band of ~1kb and a vector + ~500bp of insert band. Results do not look good. Bands seem to indicate much too large products, but will discuss with Chris tomorrow.(AH)
-
* M116 (pSB1A2+''glgC''-mut1,2) and M120 (BABEL2+''glgC''-mut1,2,3) submitted for sequencing. (CF)
+
* M116 (pSB1A2+''glgC''-mut1,2) and M120 (BABEL2+''glgC''-mut1,2,3) submitted for sequencing. (CF)<br />
 +
<br />
 +
 
 +
:::: '''[[Edinburgh/13_August_2008|Next Entry >]]'''

Latest revision as of 20:54, 29 October 2008

< Previous Entry

Week 9

Tuesday 12 August 08

  • Plate 115 made with subs from L33 (Pl. 109/110: pSB1A2+PcstA), L34 (Pl. 111/112: pSB1A2+dxs+crtE) and L35 (Pl. 113/114: pSB1A2+dxs+lims1) (CF)
  • Over-night cultures of L33 (pSB1A2+PcstA, sub-cloned on Plate 115), L34 (pSB1A2+dxs+crtE, sub-cloned on Plate 115) and L35 (pSB1A2+dxs+lims1, subcloned on Plate 115) set up, ready for minipreps tomorrow.
  • M121-M123: Minipreps of pSB1A2+crtY (1,2,3). M124-M126: Minipreps of pSB1A2+rbs+crtY (1,2,3). note: I messed up M121 by adding 200µl instead of 100µl of sol 1. They are in the green box, the orange one is full. (OG)
  • Double digests of M121 to M126, run on Gel 46. It looks good! M121 is good! (Yan)
  • Purified P61 (rrnB) for sequencing. (CF/AM)
  • Re-purified already purified genomic DNA from C. fimi. This meaningless endeavour resulted from a misunderstanding. Hopefully, the doubly-purified DNA will still be useable. (AM)
  • P57 (cex from cells) EcoRI/PstI double digest, undigested P64 (cex from genomic DNA), P66 (su1) and P67 (iso2) run on Gel 45. P57 double digest yielded no clear bands; P64 yielded a clear band at 1.5 kb. (CF/AM)
  • Purified P57 (cex from cell suspension) and P64 (cex from genomic DNA). Digested both with PstI. (AM)
  • PCR for cenA from C. fimi genomic DNA (P65): denaturing 1 min, annealing 56°C for 20s, extension 30s, with glycerol. (AM)
  • P57 and P64 (cex) PstI digests and P65 (cenA) run on Gel 47. Results indicate success! (AM)
  • Re-did the excise of crtE from BABEL2 (M79); cut out the band responsible for crtE and Edinbrick 1 on the gel, followed by putification of crtE and Edinbrick1 from the cut-out gel. Finally, ligation of crtE to Edinbrick1 (L38). (HX, AH)
  • Analytical digests as follows (AH):
    • M109 and M110 (pSB1A2+crtB+crtI): BamHI/EcoRV
    • M115 and M116 (pSB1A2+glgC-mut1,2): HindIII
    • M115 and M116 (pSB1A2+glgC-mut1,2): EcoRI/HindIII
  • Digests of M109, M110, M115 and M116 were run on gel 48. M109 and M110 should give two bands if both genes are present. HindIII digest of M115/116 should give a single band indicating linearised plasmid with glgC. Double digest of M115/116 should give an insert band of ~1kb and a vector + ~500bp of insert band. Results do not look good. Bands seem to indicate much too large products, but will discuss with Chris tomorrow.(AH)
  • M116 (pSB1A2+glgC-mut1,2) and M120 (BABEL2+glgC-mut1,2,3) submitted for sequencing. (CF)


Next Entry >
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