Edinburgh/20 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/19_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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=== Sunday 20 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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* Ran P24 and P25 on '''Gel 19'''. No amplification products. Time to do some trouble shooting. The fault is in either the primers, the template, or the reactions. All previous reactions have been fine, so most likely the primers or template. To check this, we need to do a positive control using universal primers such as fd1 and rd1 (amplify 16S rRNA gene ''rrnB'') which should definitely give a product. If these fail, then it is most likely that the template is at fault - we should prepare genomic DNA and try using this as template rather than cells; also do a Gram stain to confirm that the cells look OK. If the control reaction works, try remaking the primer solutions, though it seems unlikely that all four sets could be wrong, unless I was having a really bad day. (CF)
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var totaloffset=(offsettype=="left")? what.offsetLeft : what.offsetTop;
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* Redid digest of M48 (pSB1A2+rbs+''dxs'') with SacI/SpeI. Does not look good. Also repeated digests of clones M36 (pSB1A2+''crtB'') and M42 (pSB1A2+''crtI'') alternating single digests (EcoRI) and double digests (EcoRI/PstI) to check for inserts. Look OK. Submit for sequencing. (CF)
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var parentEl=what.offsetParent;
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* Also: I have a plan for in vitro assembly to cut down on transformations and minipreps. Could have a try of this next week if there are some students with some free time. (CF)<br />
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<br />
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parentEl=parentEl.offsetParent;
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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/21_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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this.dropmenuobj.contentmeasure=this.dropmenuobj.offsetWidth
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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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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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this.clearhidemenu()
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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.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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contains_firefox:function(a, b) {
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while (b.parentNode)
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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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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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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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+
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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")){
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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){
+
-
var event=typeof e!="undefined"? e : window.event
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tabdropdown.dropit(this, event, this.getAttribute("rel"))
+
-
}
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}
+
-
if (dselected=="auto" && typeof setalready=="undefined" && this.isSelected(menuitems[i].href)){
+
-
menuitems[i].parentNode.className+=" selected default"
+
-
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"
+
-
}
+
-
}
+
-
 
+
-
}
+
-
</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;
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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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.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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.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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.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;
+
-
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>
+
-
 
+
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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>
+
-
</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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-
 
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=== Week 5 ===
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==== Monday 14 July 08 ====
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* Digests and ligation '''L12''' to add rbs to ''appY'' clone M15 (sequence back today, seems OK).
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* Minipreps '''M31 to M42''' of ''crtB'' and ''crtI'' clones. Digests with EcoRI/PstI. (AM)
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Latest revision as of 14:09, 28 August 2008

< Previous Entry

Week 5

Sunday 20 July 08

  • Ran P24 and P25 on Gel 19. No amplification products. Time to do some trouble shooting. The fault is in either the primers, the template, or the reactions. All previous reactions have been fine, so most likely the primers or template. To check this, we need to do a positive control using universal primers such as fd1 and rd1 (amplify 16S rRNA gene rrnB) which should definitely give a product. If these fail, then it is most likely that the template is at fault - we should prepare genomic DNA and try using this as template rather than cells; also do a Gram stain to confirm that the cells look OK. If the control reaction works, try remaking the primer solutions, though it seems unlikely that all four sets could be wrong, unless I was having a really bad day. (CF)
  • Redid digest of M48 (pSB1A2+rbs+dxs) with SacI/SpeI. Does not look good. Also repeated digests of clones M36 (pSB1A2+crtB) and M42 (pSB1A2+crtI) alternating single digests (EcoRI) and double digests (EcoRI/PstI) to check for inserts. Look OK. Submit for sequencing. (CF)
  • Also: I have a plan for in vitro assembly to cut down on transformations and minipreps. Could have a try of this next week if there are some students with some free time. (CF)


Next Entry >
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