Edinburgh/11 August 2008

From 2008.igem.org

(Difference between revisions)
(→Monday 11 August 08)
Line 1: Line 1:
-
<html>
+
<div id="header">{{Template:Team:Edinburgh/Templates/notebook-entry/header}}</div>
-
<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 tabdropdown={
+
:::: '''[[Edinburgh/10_August_2008|< Previous Entry]]'''
-
disappeardelay: 200, //set delay in miliseconds before menu disappears onmouseout
+
-
disablemenuclick: false, //when user clicks on a menu item with a drop down menu, disable menu item's link?
+
-
enableiframeshim: 1, //1 or 0, for true or false
+
-
 
+
-
//No need to edit beyond here////////////////////////
+
-
dropmenuobj: null, ie: document.all, firefox: document.getElementById&&!document.all, previousmenuitem:null,
+
-
currentpageurl: window.location.href.replace("http://"+window.location.hostname, "").replace(/^\//, ""), //get current page url (minus hostname, ie: http://www.dynamicdrive.com/)
+
-
 
+
-
getposOffset:function(what, offsettype){
+
-
var totaloffset=(offsettype=="left")? what.offsetLeft : what.offsetTop;
+
-
var parentEl=what.offsetParent;
+
-
while (parentEl!=null){
+
-
totaloffset=(offsettype=="left")? totaloffset+parentEl.offsetLeft : totaloffset+parentEl.offsetTop;
+
-
parentEl=parentEl.offsetParent;
+
-
}
+
-
return totaloffset;
+
-
},
+
-
 
+
-
showhide:function(obj, e, obj2){ //obj refers to drop down menu, obj2 refers to tab menu item mouse is currently over
+
-
if (this.ie || this.firefox)
+
-
this.dropmenuobj.style.left=this.dropmenuobj.style.top="-500px"
+
-
if (e.type=="click" && obj.visibility==hidden || e.type=="mouseover"){
+
-
if (obj2.parentNode.className.indexOf("default")==-1) //if tab isn't a default selected one
+
-
obj2.parentNode.className="selected"
+
-
obj.visibility="visible"
+
-
}
+
-
else if (e.type=="click")
+
-
obj.visibility="hidden"
+
-
},
+
-
 
+
-
iecompattest:function(){
+
-
return (document.compatMode && document.compatMode!="BackCompat")? document.documentElement : document.body
+
-
},
+
-
 
+
-
clearbrowseredge:function(obj, whichedge){
+
-
var edgeoffset=0
+
-
if (whichedge=="rightedge"){
+
-
var windowedge=this.ie && !window.opera? this.standardbody.scrollLeft+this.standardbody.clientWidth-15 : window.pageXOffset+window.innerWidth-15
+
-
this.dropmenuobj.contentmeasure=this.dropmenuobj.offsetWidth
+
-
if (windowedge-this.dropmenuobj.x < this.dropmenuobj.contentmeasure)  //move menu to the left?
+
-
edgeoffset=this.dropmenuobj.contentmeasure-obj.offsetWidth
+
-
}
+
-
else{
+
-
var topedge=this.ie && !window.opera? this.standardbody.scrollTop : window.pageYOffset
+
-
var windowedge=this.ie && !window.opera? this.standardbody.scrollTop+this.standardbody.clientHeight-15 : window.pageYOffset+window.innerHeight-18
+
-
this.dropmenuobj.contentmeasure=this.dropmenuobj.offsetHeight
+
-
if (windowedge-this.dropmenuobj.y < this.dropmenuobj.contentmeasure){ //move up?
+
-
edgeoffset=this.dropmenuobj.contentmeasure+obj.offsetHeight
+
-
if ((this.dropmenuobj.y-topedge)<this.dropmenuobj.contentmeasure) //up no good either?
+
-
edgeoffset=this.dropmenuobj.y+obj.offsetHeight-topedge
+
-
}
+
-
this.dropmenuobj.firstlink.style.borderTopWidth=(edgeoffset==0)? 0 : "1px" //Add 1px top border to menu if dropping up
+
-
}
+
-
return edgeoffset
+
-
},
+
-
 
+
-
dropit:function(obj, e, dropmenuID){
+
-
if (this.dropmenuobj!=null){ //hide previous menu
+
-
this.dropmenuobj.style.visibility="hidden" //hide menu
+
-
if (this.previousmenuitem!=null && this.previousmenuitem!=obj){
+
-
if (this.previousmenuitem.parentNode.className.indexOf("default")==-1) //If the tab isn't a default selected one
+
-
this.previousmenuitem.parentNode.className=""
+
-
}
+
-
}
+
-
this.clearhidemenu()
+
-
if (this.ie||this.firefox){
+
-
obj.onmouseout=function(){tabdropdown.delayhidemenu(obj)}
+
-
obj.onclick=function(){return !tabdropdown.disablemenuclick} //disable main menu item link onclick?
+
-
this.dropmenuobj=document.getElementById(dropmenuID)
+
-
this.dropmenuobj.onmouseover=function(){tabdropdown.clearhidemenu()}
+
-
this.dropmenuobj.onmouseout=function(e){tabdropdown.dynamichide(e, obj)}
+
-
this.dropmenuobj.onclick=function(){tabdropdown.delayhidemenu(obj)}
+
-
this.showhide(this.dropmenuobj.style, e, obj)
+
-
this.dropmenuobj.x=this.getposOffset(obj, "left")
+
-
this.dropmenuobj.y=this.getposOffset(obj, "top")
+
-
this.dropmenuobj.style.left=this.dropmenuobj.x-this.clearbrowseredge(obj, "rightedge")+"px"
+
-
this.dropmenuobj.style.top=this.dropmenuobj.y-this.clearbrowseredge(obj, "bottomedge")+obj.offsetHeight+1+"px"
+
-
this.previousmenuitem=obj //remember main menu item mouse moved out from (and into current menu item)
+
-
this.positionshim() //call iframe shim function
+
-
}
+
-
},
+
-
 
+
-
contains_firefox:function(a, b) {
+
-
while (b.parentNode)
+
-
if ((b = b.parentNode) == a)
+
-
return true;
+
-
return false;
+
-
},
+
-
 
+
-
dynamichide:function(e, obj2){ //obj2 refers to tab menu item mouse is currently over
+
-
var evtobj=window.event? window.event : e
+
-
if (this.ie&&!this.dropmenuobj.contains(evtobj.toElement))
+
-
this.delayhidemenu(obj2)
+
-
else if (this.firefox&&e.currentTarget!= evtobj.relatedTarget&& !this.contains_firefox(evtobj.currentTarget, evtobj.relatedTarget))
+
-
this.delayhidemenu(obj2)
+
-
},
+
-
 
+
-
delayhidemenu:function(obj2){
+
-
this.delayhide=setTimeout(function(){tabdropdown.dropmenuobj.style.visibility='hidden'; if (obj2.parentNode.className.indexOf('default')==-1) obj2.parentNode.className=''},this.disappeardelay) //hide menu
+
-
},
+
-
 
+
-
clearhidemenu:function(){
+
-
if (this.delayhide!="undefined")
+
-
clearTimeout(this.delayhide)
+
-
},
+
-
 
+
-
positionshim:function(){ //display iframe shim function
+
-
if (this.enableiframeshim && typeof this.shimobject!="undefined"){
+
-
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
+
-
this.shimobject.style.top=this.dropmenuobj.style.top
+
-
}
+
-
this.shimobject.style.display=(this.dropmenuobj.style.visibility=="visible")? "block" : "none"
+
-
}
+
-
},
+
-
 
+
-
hideshim:function(){
+
-
if (this.enableiframeshim && typeof this.shimobject!="undefined")
+
-
this.shimobject.style.display='none'
+
-
},
+
-
 
+
-
isSelected:function(menuurl){
+
-
var menuurl=menuurl.replace("http://"+menuurl.hostname, "").replace(/^\//, "")
+
-
return (tabdropdown.currentpageurl==menuurl)
+
-
},
+
-
 
+
-
init:function(menuid, dselected){
+
-
this.standardbody=(document.compatMode=="CSS1Compat")? document.documentElement : document.body //create reference to common "body" across doctypes
+
-
var menuitems=document.getElementById(menuid).getElementsByTagName("a")
+
-
for (var i=0; i<menuitems.length; i++){
+
-
if (menuitems[i].getAttribute("rel")){
+
-
var relvalue=menuitems[i].getAttribute("rel")
+
-
document.getElementById(relvalue).firstlink=document.getElementById(relvalue).getElementsByTagName("a")[0]
+
-
menuitems[i].onmouseover=function(e){
+
-
var event=typeof e!="undefined"? e : window.event
+
-
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)
+
-
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{
+
-
display:inline;
+
-
margin:0 2px 0 0;
+
-
padding:0;
+
-
text-transform:uppercase;
+
-
}
+
-
 
+
-
 
+
-
.ddcolortabs a{
+
-
float:left;
+
-
color: white;
+
-
background: black url(media/color_tabs_left.gif) no-repeat left top;
+
-
margin:0 2px 0 0;
+
-
padding:0 0 1px 3px;
+
-
text-decoration:none;
+
-
letter-spacing: 1px;
+
-
}
+
-
 
+
-
.ddcolortabs a span{
+
-
float:left;
+
-
display:block;
+
-
background: transparent url(media/color_tabs_right.gif) no-repeat right top;
+
-
padding: 4px 8px 2px 7px;
+
-
}
+
-
 
+
-
.ddcolortabs a span{
+
-
float:none;
+
-
}
+
-
 
+
-
.ddcolortabs a:hover{
+
-
background-color: #591f20;
+
-
}
+
-
 
+
-
.ddcolortabs a:hover span{
+
-
background-color: #591f20;
+
-
}
+
-
 
+
-
.ddcolortabs .selected a, #ddcolortabs .selected a span{ /*currently selected tab*/
+
-
background-color: #591f20;
+
-
}
+
-
 
+
-
.ddcolortabsline{
+
-
clear: both;
+
-
padding: 0;
+
-
width: 100%;
+
-
height: 8px;
+
-
line-height: 8px;
+
-
background: black;
+
-
border-top: 1px solid #fff; /*Remove this to remove border between bar and tabs*/
+
-
}
+
-
 
+
-
/* ######### Style for Drop Down Menu ######### */
+
-
 
+
-
.dropmenudiv_a{
+
-
position:absolute;
+
-
top: 0;
+
-
border: 1px solid black; /*THEME CHANGE HERE*/
+
-
border-top-width: 8px; /*Top border width. Should match height of .ddcolortabsline above*/
+
-
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*/
+
-
padding: 2px 0;
+
-
text-decoration: none;
+
-
color: black;
+
-
}
+
-
 
+
-
* html .dropmenudiv_a a{ /*IE only hack*/
+
-
width: 100%;
+
-
}
+
-
 
+
-
.dropmenudiv_a a:hover{ /*THEME CHANGE HERE*/
+
-
background-color: #8a3c3d;
+
-
color: white;
+
-
}
+
-
</style>
+
-
</head>
+
-
 
+
-
<!-- CSS for Drop Down Tabs Menu #1 -->
+
-
<link rel="stylesheet" type="text/css" href="ddcolortabs.css" />
+
-
 
+
-
<div id="colortab" class="ddcolortabs">
+
-
<ul>
+
-
<li><a href="https://2008.igem.org/Team:Edinburgh" title="Home"><span>Home</span></a></li>
+
-
<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>
+
-
<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>
+
=== Week 9 ===
=== Week 9 ===
==== Monday 11 August 08 ====
==== Monday 11 August 08 ====
-
* PCR products of P55 to P58 (''cenA'' and ''cex'') were run on '''Gel 41:''' ''cex'' with KOD polymerase (P57) generated a single band of the desired size. However, ''cex'' with Velocity polymerase and ''cenA'' with both KOD or Velocity polymerase failed. (YAN)
+
* PCR products of P55-P58 (''cenA'' and ''cex'') were run on '''Gel 41:''' ''cex'' with KOD polymerase (P57) generated a single band of the desired size. However, ''cex'' with Velocity polymerase and ''cenA'' with both KOD or Velocity polymerase failed. (Yan)
-
* PCR products P61 to P63 (''rrnB'', ''cenA'', ''cex'') were run on '''Gel 42'''. Very clear band for ''rrnB'', no bands for either ''cenA'' or ''cex''. (CF)
+
* PCR products P61-P63 (''rrnB'', ''cenA'', ''cex'') were run on '''Gel 42'''. Very clear band for ''rrnB'', no bands for either ''cenA'' or ''cex''. (CF)
-
* Made '''Plate 109/110''' (Transformation of L33: pBS1A2+pCstA), '''111/112''' (transformation of L34: pBS1A2+''dxs''+''crtE'') and Plate '''113/114''' (Transformation of L35: pBS1A2+''dxs''+''lims1''). (Yan)
+
* Made '''Plates 109-110''' (Transformation of L33: pBS1A2+pCstA), '''111-112''' (transformation of L34: pBS1A2+''dxs''+''crtE'') and '''113-114''' (Transformation of L35: pBS1A2+''dxs''+''lims1''). (Yan)
-
* Maxipreps '''X9''' of pSB1A2+rbs+''dxs'' (as for M72) and '''X10''' of pSB1A2P+rbs+''appY'' (as for M82). (AM)
+
* Made maxipreps '''X9''' of pSB1A2+rbs+''dxs'' (as for M72) and '''X10''' of pSB1A2P+rbs+''appY'' (as for M82). (AM)
* Redid PCR (KOD) of ''cex'' from ''C. fimi'' genomic DNA but with 10µl 50% glycerol, denaturing 1 min, annealing 60°C for 30s and extension 30s ('''P64'''). To be run on gel tomorrow. (AM)
* Redid PCR (KOD) of ''cex'' from ''C. fimi'' genomic DNA but with 10µl 50% glycerol, denaturing 1 min, annealing 60°C for 30s and extension 30s ('''P64'''). To be run on gel tomorrow. (AM)
* Digested P57 (''cex'' from KOD PCR) with EcoRI/PstI to confirm identity of the gene. ''cex'' has a PstI restriction site near its midpoint, so this digestion should generate two segments of approximately 750bp. To be run on gel tomorrow. (AM)
* Digested P57 (''cex'' from KOD PCR) with EcoRI/PstI to confirm identity of the gene. ''cex'' has a PstI restriction site near its midpoint, so this digestion should generate two segments of approximately 750bp. To be run on gel tomorrow. (AM)
* Digests performed using EcoRI/PstI to move ''crtE'' from BABEL2 (M79) to Edinbrick1. In each case, 3µl of vector was digested in 20µl total volume. The digests were run on a gel ready for excision, but gel showed no band corresponding to ''crtE'' (see '''gel 43''' showing a single band at ~3kb for BABEL2+''crtE'' and bands at ~2.5kb and 800bp for Edinbrick1). (AH)
* Digests performed using EcoRI/PstI to move ''crtE'' from BABEL2 (M79) to Edinbrick1. In each case, 3µl of vector was digested in 20µl total volume. The digests were run on a gel ready for excision, but gel showed no band corresponding to ''crtE'' (see '''gel 43''' showing a single band at ~3kb for BABEL2+''crtE'' and bands at ~2.5kb and 800bp for Edinbrick1). (AH)
-
* '''M109-M112''' Minipreps of pSB1A2+''crtB''+''crtI'', from plates 102. '''M113-M116''' Minipreps of pSB1A2+''glgC''-mut1,2 from plate 103. '''M117-M120''' Minipreps of pSB1A2+''glgC''-mut1,2,3 from plate 94 (OG)
+
* Minipreps '''M109-M112''' (putative pSB1A2+''crtB''+''crtI'', plate 102), '''M113-M116''' (pSB1A2+''glgC''-mut1,2, plate 103) and '''M117-M120''' (pSB1A2+''glgC''-mut1,2,3, plate 94) were made. (OG)
-
* Double digestion of M109 to M120 with EcoRI/PstI, run on '''gel 44'''. M110-102 (pSB1A2+''crtB''+''crtI'') have a band at 2.5kb as expected. M109 (pSB1A2+''crtB''+''crtI'') gave a band at 3kb instead, so should be ignored from now on. (Yan)
+
* Double digests of M109-M120 with EcoRI/PstI were run on '''gel 44'''. M110-M112 (pSB1A2+''crtB''+''crtI'') have a band at 2.5kb as expected. M109 (pSB1A2+''crtB''+''crtI'') gave a band at 3kb instead, so should be ignored from now on. (Yan)
-
* Subbed white colonies from plates 105 (pSB1A2+''crtY'') and 106 (pSB1A2+rbs+''crtY'') to '''Plate 108'''. (CF)
+
* Subbed white colonies from plates 105 (pSB1A2+''crtY'') and 106 (pSB1A2+rbs+''crtY'') to '''Plate 108'''. (CF)<br />
 +
<br />
 +
 
 +
:::: '''[[Edinburgh/12_August_2008|Next Entry >]]'''

Revision as of 14:50, 28 August 2008

< Previous Entry

Week 9

Monday 11 August 08

  • PCR products of P55-P58 (cenA and cex) were run on Gel 41: cex with KOD polymerase (P57) generated a single band of the desired size. However, cex with Velocity polymerase and cenA with both KOD or Velocity polymerase failed. (Yan)
  • PCR products P61-P63 (rrnB, cenA, cex) were run on Gel 42. Very clear band for rrnB, no bands for either cenA or cex. (CF)
  • Made Plates 109-110 (Transformation of L33: pBS1A2+pCstA), 111-112 (transformation of L34: pBS1A2+dxs+crtE) and 113-114 (Transformation of L35: pBS1A2+dxs+lims1). (Yan)
  • Made maxipreps X9 of pSB1A2+rbs+dxs (as for M72) and X10 of pSB1A2P+rbs+appY (as for M82). (AM)
  • Redid PCR (KOD) of cex from C. fimi genomic DNA but with 10µl 50% glycerol, denaturing 1 min, annealing 60°C for 30s and extension 30s (P64). To be run on gel tomorrow. (AM)
  • Digested P57 (cex from KOD PCR) with EcoRI/PstI to confirm identity of the gene. cex has a PstI restriction site near its midpoint, so this digestion should generate two segments of approximately 750bp. To be run on gel tomorrow. (AM)
  • Digests performed using EcoRI/PstI to move crtE from BABEL2 (M79) to Edinbrick1. In each case, 3µl of vector was digested in 20µl total volume. The digests were run on a gel ready for excision, but gel showed no band corresponding to crtE (see gel 43 showing a single band at ~3kb for BABEL2+crtE and bands at ~2.5kb and 800bp for Edinbrick1). (AH)
  • Minipreps M109-M112 (putative pSB1A2+crtB+crtI, plate 102), M113-M116 (pSB1A2+glgC-mut1,2, plate 103) and M117-M120 (pSB1A2+glgC-mut1,2,3, plate 94) were made. (OG)
  • Double digests of M109-M120 with EcoRI/PstI were run on gel 44. M110-M112 (pSB1A2+crtB+crtI) have a band at 2.5kb as expected. M109 (pSB1A2+crtB+crtI) gave a band at 3kb instead, so should be ignored from now on. (Yan)
  • Subbed white colonies from plates 105 (pSB1A2+crtY) and 106 (pSB1A2+rbs+crtY) to Plate 108. (CF)


Next Entry >
Retrieved from "http://2008.igem.org/Edinburgh/11_August_2008"