Team:Heidelberg/Toolbox Guide

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<style type="text/css">
<style type="text/css">
#myContainer {
#myContainer {
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<div class="row toolbox-icons-bar">
<div class="row toolbox-icons-bar">
<div class="col-lg-2 col-lg-offset-1 col-md-offset-1 col-md-2 col-sm-4 col-xs-6">
<div class="col-lg-2 col-lg-offset-1 col-md-offset-1 col-md-2 col-sm-4 col-xs-6">
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<a href="https://2014.igem.org/Team:Heidelberg/Toolbox/Circularization"><span class="col-lg-offset-3 col-lg-6 col-md-offset-2 col-md-8 col-sm-12 nopadding nofloat"><img src="/wiki/images/5/58/Heidelberg_Toolbox_Circularization.png" class="img-responsive" /></span>CIRCULARIZE</a>
+
<a href="https://2014.igem.org/Team:Heidelberg/Toolbox_Guide/Circularization"><span class="col-lg-offset-3 col-lg-6 col-md-offset-2 col-md-8 col-sm-12 nopadding nofloat"><img src="/wiki/images/5/58/Heidelberg_Toolbox_Circularization.png" class="img-responsive" /></span>CIRCULARIZE</a>
</div>
</div>
<div class="col-lg-2 col-md-2 col-sm-4 col-xs-6">
<div class="col-lg-2 col-md-2 col-sm-4 col-xs-6">
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<a href="https://2014.igem.org/Team:Heidelberg/Toolbox/Oligomerization"><span class="col-lg-offset-3 col-lg-6 col-md-offset-2 col-md-8 col-sm-12 nopadding nofloat"><img src="/wiki/images/4/40/Oligomerization.png" class="img-responsive" /></span>OLIGOMERIZE</a>
+
<a href="https://2014.igem.org/Team:Heidelberg/Toolbox_Guide/Localization"><span class="col-lg-offset-3 col-lg-6 col-md-offset-2 col-md-8 col-sm-12 nopadding nofloat"><img src="/wiki/images/3/3a/Heidelberg_Localize_button.png" class="img-responsive" /></span>LOCALIZE</a>
</div>
</div>
<div class="col-lg-2 col-md-2 col-sm-4 col-xs-6">
<div class="col-lg-2 col-md-2 col-sm-4 col-xs-6">
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<a href="https://2014.igem.org/Team:Heidelberg/Toolbox/Fusion"><span class="col-lg-offset-3 col-lg-6 col-md-offset-2 col-md-8 col-sm-12 nopadding nofloat"><img src="/wiki/images/8/87/Heidelberg_Toolbox_Fusion.png" class="img-responsive" /></span>FUSE & TAG</a>
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<a href="https://2014.igem.org/Team:Heidelberg/Toolbox_Guide/Fusion"><span class="col-lg-offset-3 col-lg-6 col-md-offset-2 col-md-8 col-sm-12 nopadding nofloat"><img src="/wiki/images/8/87/Heidelberg_Toolbox_Fusion.png" class="img-responsive" /></span>ATTACH</a>
</div>
</div>
<div class="col-lg-2 col-md-2 col-sm-4 col-xs-6">
<div class="col-lg-2 col-md-2 col-sm-4 col-xs-6">
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<a href="https://2014.igem.org/Team:Heidelberg/Toolbox/Purification"><span class="col-lg-offset-3 col-lg-6 col-md-offset-2 col-md-8 col-sm-12 nopadding nofloat"><img src="/wiki/images/0/04/Heidelberg_Toolbox_Purification.png" class="img-responsive" /></span>PURIFY</a>
+
<a href="https://2014.igem.org/Team:Heidelberg/Toolbox_Guide/Purification"><span class="col-lg-offset-3 col-lg-6 col-md-offset-2 col-md-8 col-sm-12 nopadding nofloat"><img src="/wiki/images/0/04/Heidelberg_Toolbox_Purification.png" class="img-responsive" /></span>PURIFY</a>
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</div>
+
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<div class="col-lg-2 col-md-2 col-sm-4 col-xs-6">
+
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<a href="https://2014.igem.org/Team:Heidelberg/Toolbox/OnOff"><span class="col-lg-offset-3 col-lg-6 col-md-offset-2 col-md-8 col-sm-12 nopadding nofloat"><img src="/wiki/images/c/c2/Heidelberg_Toolbox_On-Off.png" class="img-responsive" /></span>ACTIVATE &<br />DEACTIVATE</a>
+
</div>
</div>
 +
<!--<div class="col-lg-2 col-md-2 col-sm-4 col-xs-6">
 +
<a href="https://2014.igem.org/Team:Heidelberg/Toolbox_Guide/OnOff"><span class="col-lg-offset-3 col-lg-6 col-md-offset-2 col-md-8 col-sm-12 nopadding nofloat"><img src="/wiki/images/c/c2/Heidelberg_Toolbox_On-Off.png" class="img-responsive" /></span>ACTIVATE &<br />DEACTIVATE</a>
 +
</div>-->
</div>
</div>
-
<div class="col-lg-12">
 
-
<div class="panel panel-default">
 
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<div class="panel-heading">
 
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<h3 class="panel-title">1. Please go to <a href="http://www.rcsb.org/">www.rcsb.org</a> and get a pdb file of your protein. If you cannot find one, we will not be able to assist you circularizing it.</h3>
 
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</div>
 
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Additionally, check the DNA sequence of your proteins for EcoRI, XbaI, SpeI, PstI and BsaI recognition sites. If there are E/X/S/P sites, you might have problems to change your backbone or add a promotor. If there is a BsaI recognition site, the cloning will be more difficult.
 
-
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: data.hasBsaI, checkedValue: false, click: data.q0A.bind(null, true)" />
 
-
There is no BsaI site.
 
-
</label>
 
-
</div>
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: data.hasBsaI, checkedValue: true, click: data.q0A.bind(null, true)" />
 
-
There is a BsaI site.
 
-
</label>
 
-
</div>
 
-
</div>
 
-
 
-
<div class="panel panel-default" data-bind="if: data.q0A">
 
-
<div class="panel-heading">
 
-
<h3 class="panel-title">2. Do you want to use split inteins or sortase to circularize your protein?</h3>
 
-
</div>
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: data.useSortase, checkedValue: false, click: data.q1A.bind(null, true)" />
 
-
NpuDnaE intein RFC <span data-bind="value: RFCnumber"></span> circularization construct
 
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</label>
 
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<ul>
 
-
<li>Successfully used in our project</li>
 
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<li>High efficiency</li>
 
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<li>In vivo circularization</li>
 
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</ul>
 
-
</div>
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: data.useSortase, checkedValue: true, click: data.q1A.bind(null, true)" />
 
-
Sortase A circularization construct
 
-
</label>
 
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<ul>
 
-
<li>In vitro only</li>
 
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<li>Well-purified protein required</li>
 
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<li>Not successfully tested yet</li>
 
-
</ul>
 
-
</div>
 
-
</div>
 
-
 
-
<div class="panel panel-default" data-bind="if: data.q1A">
 
-
<div class="panel-heading">
 
-
<h3 class="panel-title">3. Can your protein be easily expressed in <i>E. coli</i>?</h3>
 
-
</div>
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: data.needsSmt3, checkedValue: false, click: data.q2A.bind(null, true)" />
 
-
Yes, no problem.
 
-
</label>
 
-
</div>
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: data.needsSmt3, checkedValue: true, click: data.q2A.bind(null, true)" />
 
-
No, I will have to add <a href="http://parts.igem.org/Part:BBa_K1362429">Smt3</a>.
 
-
</label>
 
-
</div>
 
-
</div>
 
-
 
-
<div class="panel panel-default" data-bind="if: data.q2A() &amp;&amp; !data.useSortase()">
 
-
<div class="panel-heading">
 
-
<h3 class="panel-title">4. Which exteins do you want to use? They will remain as scars in your circular protein.</h3>
 
-
</div>
 
-
<!-- ko foreach: availableExteins -->
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: $parent.data.exteins, checkedValue: $data, click: $parent.data.q3A.bind(null, true)" />
 
-
<span data-bind="text: N"></span>/<span data-bind="text: C"></span>
 
-
<!-- ko if: comment -->
 
-
(<span data-bind="text: comment"></span>)
 
-
<!-- /ko -->
 
-
<ul data-bind="foreach: notes">
 
-
<li data-bind="text: $data"></li>
 
-
</ul>
 
-
</label>
 
</div>
</div>
-
<!-- /ko -->
 
</div>
</div>
-
 
-
<div class="panel panel-default" data-bind="if: data.q3A() || (data.q2A() &amp;&amp; data.useSortase())">
 
-
<div class="panel-heading">
 
-
<h3 class="panel-title"><span data-bind="text: data.useSortase() ? 4 : 5"></span>. If you want to save time, check manually whether the ends are close together (approx. <span data-bind="text: !data.useSortase() &amp;&amp; data.exteins().N == 'XXX' ? 5 : 15"></span>&thinsp;&Aring; or closer). For example, you can use the <a href="http://spdbv.vital-it.ch/">Swiss-PdbViewer</a> or <a href="http://www.pymol.org/">PyMOL</a>.</h3>
 
-
</div>
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: data.endsAreClose, checkedValue: true, click: data.q4A.bind(null, true)" />
 
-
They are close together.
 
-
</label>
 
-
</div>
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: data.endsAreClose, checkedValue: false, click: data.q4A.bind(null, true)" />
 
-
I want/have to use <span data-bind="text: softwareName"></span>.
 
-
</label>
 
-
</div>
 
-
</div>
 
-
 
-
<div data-bind="if: data.q4A() &amp;&amp; !data.endsAreClose()">
 
-
Please use <span data-bind="text: softwareName"></span> to generate a linker for your circular protein. [LINK]
 
-
 
-
This step might take up to 11 days.
 
-
 
-
NILS – hier könnte dein instruction-file-ersatz stehen
 
-
 
-
 
-
NILS – hier auch
 
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-
 
-
NILS – hier immernoch
 
-
 
-
 
-
NILS – hier ebnfalls und auch gerne noch umfangreicher
 
-
 
-
 
-
Please save this link:<br />
 
-
<code>https://2014.igem.org/{{PAGENAME}}#<span data-bind="text: comeBackHash"></span></code>
 
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In order to generate your linker, <span data-bind="text: softwareName"></span> needs to know the scar amino acid sequence that is caused by circularization. In your case, it is <span data-bind="text: data.useSortase() ? 'LPETG' : data.exteins().N == 'XXX' ? 'just C' : (data.exteins().N + data.exteins().C)"></span>.
 
-
</div>
 
-
 
-
<div class="panel panel-default" data-bind="if: data.comingBack">
 
-
<div class="panel-heading">
 
-
<h3 class="panel-title"><span data-bind="text: data.useSortase() ? 5 : 6"></span>. Hello again. What is the result of <span data-bind="text: softwareName"></span>?</h3>
 
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</div>
 
-
<div class="radio">
 
-
<label>
 
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<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 0, click: data.q5A.bind(null, true)" />
 
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I do not need a linker.
 
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</label>
 
-
</div>
 
-
<div class="radio">
 
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<label>
 
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<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 1, click: data.q5A.bind(null, true)" />
 
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The linker + scars are &lt; 15 amino acids in length.
 
-
</label>
 
-
</div>
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 2, click: data.q5A.bind(null, true)" />
 
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The linker + scars are betweeen 16 and 30 amino acids in length.
 
-
</label>
 
-
</div>
 
-
<div class="radio">
 
-
<label>
 
-
<input type="radio" data-bind="checked: data.linkerLength, checkedValue: 3, click: data.q5A.bind(null, true)" />
 
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The linker + scars are &gt; 30 amino acids in length.
 
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</label>
 
-
</div>
 
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</div>
 
-
 
-
<div class="panel panel-default" data-bind="if: data.q5A">
 
-
<div class="panel-heading">
 
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<h3 class="panel-title"><span data-bind="text: data.useSortase() ? 6 : 7"></span>. Have you decided to use one linker or try different linkers?</h3>
 
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</div>
 
-
<div class="radio">
 
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<label>
 
-
<input type="radio" data-bind="checked: data.testSeveral, checkedValue: false, click: data.q6A.bind(null, true)" />
 
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I trust <span data-bind="text: softwareName"></span>. One should be enough.
 
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</label>
 
-
</div>
 
-
<div class="radio">
 
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<label>
 
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<input type="radio" data-bind="checked: data.testSeveral, checkedValue: true, click: data.q6A.bind(null, true)" />
 
-
I want to test several linkers.
 
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</label>
 
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</div>
 
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</div>
 
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</div>
 
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</div>
 
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</div>
 
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-
<script type="text/javascript">
 
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function CircularizationViewModel(hash) {
 
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var self = this;
 
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self.RFCnumber = '[???]';
 
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self.softwareName = '[hoffentlich nicht LinkIT]';
 
-
self.availableExteins = [
 
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{ N: 'RGK', C: 'CWE', comment: '', notes: ['Efficient, tested by us', 'Large scar'] },
 
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{ N: 'RGT', C: 'CWE', comment: '', notes: ['Efficient, tested by us', 'Large scar'] },
 
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{ N: 'AEY', C: 'CFN' , comment: '', notes: ['Efficient, native extein', 'Large scar'] },
 
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{ N: 'XXX', C: 'CXX', comment: 'X = native amino acids of the protein', notes: ['Probably less efficient (depends on the protein)', 'Small scar'] },
 
-
];
 
-
 
-
var data = hash && $.parseJSON($.base64.decode(hash.substr(1)));
 
-
self.data = {
 
-
comingBack: data ? data.comingBack : false,
 
-
q0A: ko.observable(data ? data.q0A : false),
 
-
hasBsaI: ko.observable(data && data.hasBsaI),
 
-
q1A: ko.observable(data ? data.q1A : false),
 
-
useSortase: ko.observable(data && data.useSortase),
 
-
q2A: ko.observable(data ? data.q2A : false),
 
-
needsSmt3: ko.observable(data && data.needsSmt3),
 
-
q3A: ko.observable(data ? data.q3A : false),
 
-
exteins: ko.observable(data && data.exteins),
 
-
q4A: ko.observable(data ? data.q4A : false),
 
-
endsAreClose: ko.observable(data && data.endsAreClose),
 
-
q5A: ko.observable(data ? data.q5A : false),
 
-
linkerLength: ko.observable(data && data.linkerLength),
 
-
q6A: ko.observable(data ? data.q6A : false),
 
-
testSeveral: ko.observable(data && data.testSeveral),
 
-
};
 
-
 
-
self.hash = ko.computed(function () {
 
-
self.data.q0A();
 
-
self.data.q1A();
 
-
self.data.q2A();
 
-
self.data.q3A();
 
-
self.data.q4A();
 
-
self.data.q5A();
 
-
self.data.q6A();
 
-
self.data.hasBsaI();
 
-
self.data.useSortase();
 
-
self.data.needsSmt3();
 
-
self.data.exteins();
 
-
self.data.endsAreClose();
 
-
self.data.linkerLength();
 
-
self.data.testSeveral();
 
-
 
-
window.location.hash = $.base64.encode(ko.toJSON(self.data));
 
-
console.log(window.location.hash, ko.toJSON(self.data));
 
-
return window.location.hash;
 
-
 
-
if (self.q0A()) {
 
-
window.location.hash = '#' + (self.hasBsaI() ? '1': '0');
 
-
 
-
if (self.q1A()) {
 
-
window.location.hash += self.useSortase() ? '1': '0';
 
-
 
-
if (self.q2A()) {
 
-
window.location.hash += self.needsSmt3() ? '1': '0';
 
-
 
-
if (self.q3A() && !self.useSortase())
 
-
window.location.hash += self.exteins().N;
 
-
 
-
if (self.q4A()) {
 
-
window.location.hash += self.endsAreClose() ? '1': '0';
 
-
 
-
if (self.q5A()) {
 
-
window.location.hash += self.linkerLength();
 
-
 
-
if (self.q6A()) {
 
-
window.location.hash += self.testSeveral() ? '1': '0';
 
-
}
 
-
}
 
-
}
 
-
}
 
-
}
 
-
} else {
 
-
window.location.hash = '';
 
-
}
 
-
 
-
return window.location.hash;
 
-
});
 
-
 
-
self.comeBackHash = ko.computed(function () {
 
-
var tmp = self.data.comingBack;
 
-
self.data.comingBack = true;
 
-
var hash = $.base64.encode(ko.toJSON(self.data));
 
-
self.data.comingBack = tmp;
 
-
return hash;
 
-
});
 
-
}
 
-
 
-
vm = new CircularizationViewModel(window.location.hash);
 
-
ko.applyBindings(vm);
 
-
 
-
/*function parseHash(hash) {
 
-
var data = hash.substring(1);
 
-
for(i = 0; i< data.length; i++) {
 
-
switch(i){
 
-
case 1:
 
-
vm.hasBsaI(data[i]);
 
-
break;
 
-
case 2:
 
-
vm.
 
-
}
 
-
}
 
-
}*/
 
-
</script>
 
</html>
</html>

Latest revision as of 03:43, 18 October 2014

Retrieved from "http://2014.igem.org/Team:Heidelberg/Toolbox_Guide"