Difference between revisions of "Team:TU Dresden/Notebook/LabJournal"
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Revision as of 21:35, 12 September 2015
//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" />
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 $('').prependTo(this) $('').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'))
Lab Journal
- 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.
- 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.
- 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.
- 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.