Difference between revisions of "Team:TU Dresden/Notebook/LabJournal"

Line 41: Line 41:
  
 
</style>
 
</style>
<script type="text/javascript">
+
<script type="text/javascript" src="https://2015.igem.org/Team:TU_Dresden/codenotebook?action=raw&amp;ctype=text/js">
//** Accordion Content script: By Dynamic Drive, at http://www.dynamicdrive.com
+
//** Created: Jan 7th, 08'. Last updated: June 7th, 2010 to v1.9
+
 
+
//Version 1.9: June 7th, 2010':
+
//**1) Ajax content support added, so a given header's content can be dynamically fetched from an external file and on demand.
+
//**2) Optimized script performance by caching header and content container references
+
 
+
 
+
var ddaccordion={
+
ajaxloadingmsg: '<img src="http://www.dynamicdrive.com/dynamicindex17/loading2.gif" /><br />Loading Content...', //customize HTML to output while Ajax content is being fetched (if applicable)
+
 
+
headergroup: {}, //object to store corresponding header group based on headerclass value
+
contentgroup: {}, //object to store corresponding content group based on headerclass value
+
 
+
preloadimages:function($images){
+
$images.each(function(){
+
var preloadimage=new Image()
+
preloadimage.src=this.src
+
})
+
},
+
 
+
expandone:function(headerclass, selected){ //PUBLIC function to expand a particular header
+
this.toggleone(headerclass, selected, "expand")
+
},
+
 
+
collapseone:function(headerclass, selected){ //PUBLIC function to collapse a particular header
+
this.toggleone(headerclass, selected, "collapse")
+
},
+
 
+
expandall:function(headerclass){ //PUBLIC function to expand all headers based on their shared CSS classname
+
var $headers=this.headergroup[headerclass]
+
this.contentgroup[headerclass].filter(':hidden').each(function(){
+
$headers.eq(parseInt($(this).attr('contentindex'))).trigger("evt_accordion")
+
})
+
},
+
 
+
collapseall:function(headerclass){ //PUBLIC function to collapse all headers based on their shared CSS classname
+
var $headers=this.headergroup[headerclass]
+
this.contentgroup[headerclass].filter(':visible').each(function(){
+
$headers.eq(parseInt($(this).attr('contentindex'))).trigger("evt_accordion")
+
})
+
},
+
 
+
toggleone:function(headerclass, selected, optstate){ //PUBLIC function to expand/ collapse a particular header
+
var $targetHeader=this.headergroup[headerclass].eq(selected)
+
var $subcontent=this.contentgroup[headerclass].eq(selected)
+
if (typeof optstate=="undefined" || optstate=="expand" && $subcontent.is(":hidden") || optstate=="collapse" && $subcontent.is(":visible"))
+
$targetHeader.trigger("evt_accordion")
+
},
+
 
+
ajaxloadcontent:function($targetHeader, $targetContent, config, callback){
+
var ajaxinfo=$targetHeader.data('ajaxinfo')
+
 
+
function handlecontent(content){ //nested function
+
if (content){ //if ajax content has loaded
+
ajaxinfo.cacheddata=content //remember ajax content
+
ajaxinfo.status="cached" //set ajax status to cached
+
if ($targetContent.queue("fx").length==0){ //if this content isn't currently expanding or collapsing
+
$targetContent.hide().html(content) //hide loading message, then set sub content's HTML to ajax content
+
ajaxinfo.status="complete" //set ajax status to complete
+
callback() //execute callback function- expand this sub content
+
}
+
}
+
if (ajaxinfo.status!="complete"){
+
setTimeout(function(){handlecontent(ajaxinfo.cacheddata)}, 100) //call handlecontent() again until ajax content has loaded (ajaxinfo.cacheddata contains data)
+
}
+
} //end nested function
+
 
+
if (ajaxinfo.status=="none"){ //ajax data hasn't been fetched yet
+
$targetContent.html(this.ajaxloadingmsg)
+
$targetContent.slideDown(config.animatespeed)
+
ajaxinfo.status="loading" //set ajax status to "loading"
+
$.ajax({
+
url: ajaxinfo.url, //path to external menu file
+
error:function(ajaxrequest){
+
handlecontent('Error fetching content. Server Response: '+ajaxrequest.responseText)
+
},
+
success:function(content){
+
content=(content=="")? " " : content //if returned content is empty, set it to "space" is content no longer returns false/empty (hasn't loaded yet)
+
handlecontent(content)
+
}
+
})
+
}
+
else if (ajaxinfo.status=="loading")
+
handlecontent(ajaxinfo.cacheddata)
+
},
+
 
+
expandit:function($targetHeader, $targetContent, config, useractivated, directclick, skipanimation){
+
var ajaxinfo=$targetHeader.data('ajaxinfo')
+
if (ajaxinfo){ //if this content should be fetched via Ajax
+
if (ajaxinfo.status=="none" || ajaxinfo.status=="loading")
+
this.ajaxloadcontent($targetHeader, $targetContent, config, function(){ddaccordion.expandit($targetHeader, $targetContent, config, useractivated, directclick)})
+
else if (ajaxinfo.status=="cached"){
+
$targetContent.html(ajaxinfo.cacheddata)
+
ajaxinfo.cacheddata=null
+
ajaxinfo.status="complete"
+
}
+
}
+
this.transformHeader($targetHeader, config, "expand")
+
$targetContent.slideDown(skipanimation? 0 : config.animatespeed, function(){
+
config.onopenclose($targetHeader.get(0), parseInt($targetHeader.attr('headerindex')), $targetContent.css('display'), useractivated)
+
if (config.postreveal=="gotourl" && directclick){ //if revealtype is "Go to Header URL upon click", and this is a direct click on the header
+
var targetLink=($targetHeader.is("a"))? $targetHeader.get(0) : $targetHeader.find('a:eq(0)').get(0)
+
if (targetLink) //if this header is a link
+
setTimeout(function(){location=targetLink.href}, 200) //ignore link target, as window.open(targetLink, targetLink.target) doesn't work in FF if popup blocker enabled
+
}
+
})
+
},
+
 
+
collapseit:function($targetHeader, $targetContent, config, isuseractivated){
+
this.transformHeader($targetHeader, config, "collapse")
+
$targetContent.slideUp(config.animatespeed, function(){config.onopenclose($targetHeader.get(0), parseInt($targetHeader.attr('headerindex')), $targetContent.css('display'), isuseractivated)})
+
},
+
 
+
transformHeader:function($targetHeader, config, state){
+
$targetHeader.addClass((state=="expand")? config.cssclass.expand : config.cssclass.collapse) //alternate btw "expand" and "collapse" CSS classes
+
.removeClass((state=="expand")? config.cssclass.collapse : config.cssclass.expand)
+
if (config.htmlsetting.location=='src'){ //Change header image (assuming header is an image)?
+
$targetHeader=($targetHeader.is("img"))? $targetHeader : $targetHeader.find('img').eq(0) //Set target to either header itself, or first image within header
+
$targetHeader.attr('src', (state=="expand")? config.htmlsetting.expand : config.htmlsetting.collapse) //change header image
+
}
+
else if (config.htmlsetting.location=="prefix") //if change "prefix" HTML, locate dynamically added ".accordprefix" span tag and change it
+
$targetHeader.find('.accordprefix').html((state=="expand")? config.htmlsetting.expand : config.htmlsetting.collapse)
+
else if (config.htmlsetting.location=="suffix")
+
$targetHeader.find('.accordsuffix').html((state=="expand")? config.htmlsetting.expand : config.htmlsetting.collapse)
+
},
+
 
+
urlparamselect:function(headerclass){
+
var result=window.location.search.match(new RegExp(headerclass+"=((\\d+)(,(\\d+))*)", "i")) //check for "?headerclass=2,3,4" in URL
+
if (result!=null)
+
result=RegExp.$1.split(',')
+
return result //returns null, [index], or [index1,index2,etc], where index are the desired selected header indices
+
},
+
 
+
getCookie:function(Name){
+
var re=new RegExp(Name+"=[^;]+", "i") //construct RE to search for target name/value pair
+
if (document.cookie.match(re)) //if cookie found
+
return document.cookie.match(re)[0].split("=")[1] //return its value
+
return null
+
},
+
 
+
setCookie:function(name, value){
+
document.cookie = name + "=" + value + "; path=/"
+
},
+
 
+
init:function(config){
+
document.write('<style type="text/css">\n')
+
document.write('.'+config.contentclass+'{display: none}\n') //generate CSS to hide contents
+
document.write('a.hiddenajaxlink{display: none}\n') //CSS class to hide ajax link
+
document.write('<\/style>')
+
jQuery(document).ready(function($){
+
ddaccordion.urlparamselect(config.headerclass)
+
var persistedheaders=ddaccordion.getCookie(config.headerclass)
+
ddaccordion.headergroup[config.headerclass]=$('.'+config.headerclass) //remember header group for this accordion
+
ddaccordion.contentgroup[config.headerclass]=$('.'+config.contentclass) //remember content group for this accordion
+
var $headers=ddaccordion.headergroup[config.headerclass]
+
var $subcontents=ddaccordion.contentgroup[config.headerclass]
+
config.cssclass={collapse: config.toggleclass[0], expand: config.toggleclass[1]} //store expand and contract CSS classes as object properties
+
config.revealtype=config.revealtype || "click"
+
config.revealtype=config.revealtype.replace(/mouseover/i, "mouseenter")
+
if (config.revealtype=="clickgo"){
+
config.postreveal="gotourl" //remember added action
+
config.revealtype="click" //overwrite revealtype to "click" keyword
+
}
+
if (typeof config.togglehtml=="undefined")
+
config.htmlsetting={location: "none"}
+
else
+
config.htmlsetting={location: config.togglehtml[0], collapse: config.togglehtml[1], expand: config.togglehtml[2]} //store HTML settings as object properties
+
config.oninit=(typeof config.oninit=="undefined")? function(){} : config.oninit //attach custom "oninit" event handler
+
config.onopenclose=(typeof config.onopenclose=="undefined")? function(){} : config.onopenclose //attach custom "onopenclose" event handler
+
var lastexpanded={} //object to hold reference to last expanded header and content (jquery objects)
+
var expandedindices=ddaccordion.urlparamselect(config.headerclass) || ((config.persiststate && persistedheaders!=null)? persistedheaders : config.defaultexpanded)
+
if (typeof expandedindices=='string') //test for string value (exception is config.defaultexpanded, which is an array)
+
expandedindices=expandedindices.replace(/c/ig, '').split(',') //transform string value to an array (ie: "c1,c2,c3" becomes [1,2,3]
+
if (expandedindices.length==1 && expandedindices[0]=="-1") //check for expandedindices value of [-1], indicating persistence is on and no content expanded
+
expandedindices=[]
+
if (config["collapseprev"] && expandedindices.length>1) //only allow one content open?
+
expandedindices=[expandedindices.pop()] //return last array element as an array (for sake of jQuery.inArray())
+
if (config["onemustopen"] && expandedindices.length==0) //if at least one content should be open at all times and none are, open 1st header
+
expandedindices=[0]
+
$headers.each(function(index){ //loop through all headers
+
var $header=$(this)
+
if (/(prefix)|(suffix)/i.test(config.htmlsetting.location) && $header.html()!=""){ //add a SPAN element to header depending on user setting and if header is a container tag
+
$('<span class="accordprefix"></span>').prependTo(this)
+
$('<span class="accordsuffix"></span>').appendTo(this)
+
}
+
$header.attr('headerindex', index+'h') //store position of this header relative to its peers
+
$subcontents.eq(index).attr('contentindex', index+'c') //store position of this content relative to its peers
+
var $subcontent=$subcontents.eq(index)
+
var $hiddenajaxlink=$subcontent.find('a.hiddenajaxlink:eq(0)') //see if this content should be loaded via ajax
+
if ($hiddenajaxlink.length==1){
+
$header.data('ajaxinfo', {url:$hiddenajaxlink.attr('href'), cacheddata:null, status:'none'}) //store info about this ajax content inside header
+
}
+
var needle=(typeof expandedindices[0]=="number")? index : index+'' //check for data type within expandedindices array- index should match that type
+
if (jQuery.inArray(needle, expandedindices)!=-1){ //check for headers that should be expanded automatically (convert index to string first)
+
ddaccordion.expandit($header, $subcontent, config, false, false, !config.animatedefault) //3rd last param sets 'isuseractivated' parameter, 2nd last sets isdirectclick, last sets skipanimation param
+
lastexpanded={$header:$header, $content:$subcontent}
+
}  //end check
+
else{
+
$subcontent.hide()
+
config.onopenclose($header.get(0), parseInt($header.attr('headerindex')), $subcontent.css('display'), false) //Last Boolean value sets 'isuseractivated' parameter
+
ddaccordion.transformHeader($header, config, "collapse")
+
}
+
})
+
$headers.bind("evt_accordion", function(e, isdirectclick){ //assign CUSTOM event handler that expands/ contacts a header
+
var $subcontent=$subcontents.eq(parseInt($(this).attr('headerindex'))) //get subcontent that should be expanded/collapsed
+
if ($subcontent.css('display')=="none"){
+
ddaccordion.expandit($(this), $subcontent, config, true, isdirectclick) //2nd last param sets 'isuseractivated' parameter
+
if (config["collapseprev"] && lastexpanded.$header && $(this).get(0)!=lastexpanded.$header.get(0)){ //collapse previous content?
+
ddaccordion.collapseit(lastexpanded.$header, lastexpanded.$content, config, true) //Last Boolean value sets 'isuseractivated' parameter
+
}
+
lastexpanded={$header:$(this), $content:$subcontent}
+
}
+
else if (!config["onemustopen"] || config["onemustopen"] && lastexpanded.$header && $(this).get(0)!=lastexpanded.$header.get(0)){
+
ddaccordion.collapseit($(this), $subcontent, config, true) //Last Boolean value sets 'isuseractivated' parameter
+
}
+
})
+
$headers.bind(config.revealtype, function(){
+
if (config.revealtype=="mouseenter"){
+
clearTimeout(config.revealdelay)
+
var headerindex=parseInt($(this).attr("headerindex"))
+
config.revealdelay=setTimeout(function(){ddaccordion.expandone(config["headerclass"], headerindex)}, config.mouseoverdelay || 0)
+
}
+
else{
+
$(this).trigger("evt_accordion", [true]) //last parameter indicates this is a direct click on the header
+
return false //cancel default click behavior
+
}
+
})
+
$headers.bind("mouseleave", function(){
+
clearTimeout(config.revealdelay)
+
})
+
config.oninit($headers.get(), expandedindices)
+
$(window).bind('unload', function(){ //clean up and persist on page unload
+
$headers.unbind()
+
var expandedindices=[]
+
$subcontents.filter(':visible').each(function(index){ //get indices of expanded headers
+
expandedindices.push($(this).attr('contentindex'))
+
})
+
if (config.persiststate==true && $headers.length>0){ //persist state?
+
expandedindices=(expandedindices.length==0)? '-1c' : expandedindices //No contents expanded, indicate that with dummy '-1c' value?
+
ddaccordion.setCookie(config.headerclass, expandedindices)
+
}
+
})
+
})
+
}
+
}
+
 
+
//preload any images defined inside ajaxloadingmsg variable
+
ddaccordion.preloadimages(jQuery(ddaccordion.ajaxloadingmsg).filter('img'))
+
 
</script>
 
</script>
<script type="text/javascript">
+
<<script type="text/javascript">
  
 
//Initialize 2nd demo:
 
//Initialize 2nd demo:

Revision as of 21:45, 12 September 2015



<

Lab Journal

[Collapse all] | [Expand all]

Week 1: (20-26 July)
  • Plasmids were received (T18, ZHER2, LZT18, LZT25 and HER2 codon) and diluted. Also two pSB1C3 plasmids from iGEM containing RBS (BBa_E0020) and CFP (BBa_E0020) were diluted.
  • Preparation of E. coli GB05 and set cultures overnight.
  • Electroporation of the cells with the plasmids.
  • Transfected cells were streaked out on chloramphenicol (Cm) and kanamycin (kan) plates.
  • Colonies were picked and mixed with Cm and kan. These were stored in the fridge.
  • Streaking out colonies from DHM1, BTH101 and K12 plates.
Week 2 (27 July-2 August)
  • A miniprep was done with the seven cultures with the plasmids. A glycerol stock of each culture was saved.
  • The concentration of the plasmids was measured using the nanodrop.
  • A digestion of the plasmids was done and a gel was run.
Week 3 (3-9 August)
  • 3 cultures for GB05 and K12 were set overnight.
  • Transformation of T25 and gene III plasmids and promoter (pLac) in E. coli: gene III in GB05 and K12; T25 in GB05; promoter in K12 and GB05.
  • Transformed colonies were plated on kan plates (gIII and T25) and Cm (pLac). A miniprerp was done with the overnight cultures of pLac, T25 and gIII. The concentration of plasmid was measured with the nanodrop.
  • New back-up cultures were set overnight.
  • Cloning of P3 and RBS+CFP in pLac, followed by dephosphorylation and gel running and purification. The concentration was measured with the nanodrop. pET28a vector preparation: digestion and dephosphorylation. Afterwards a gel was run and the DNA was extracted.
  • A PCR was set to create HER2 with NheI and NotI restriction sites. A digestion was done and the product was run on a gel and purified. The concentration was measured with the nanodrop. This process was repeated some days later since the concentration was too low.
Week 4 (10-16 August)
  • Ligation of pLac + P3 and RBS + CFP: first set up the cultures for transformation, and the transform the electrocompetent cells: pLac in K12, pLac+P3 in K12 and GB05, and RBS+CFP in GB05. Plate the transformed cells and incubate them overnight.
  • Restriction digestion for the biobrick constructs and BACTH buildup: ZHER2, HER2, LZT25, LZT18, T18, T25 and P3.
  • Restriction digestion of HER2 and pET28a. The products were run on a gel and afterwards the weight was measured.
  • Preparation of the plates needed for the setup: one colony of pLac in K12 and pLac+pIII in K12 were streaked out and incubated in Cm+LB.
  • Plasmid miniprep from RBS+CFP in GB05 and pLac+P3 in GB05. The concentration of the plasmids was measured with the nanodrop. The products were then digested, dephosphorylated and loaded on a gel.
Week 5 ()
Week 6 ()
Week 7 ()