Team:BostonU

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<body>
<body>
Line 519: Line 28:
<!--Navibar-->
<!--Navibar-->
<ul id="nav">  
<ul id="nav">  
-
<li><a href="">TEAM</a>
+
<li><a href="https://2014.igem.org/Team:BostonU/Team">TEAM</a>
-
<ul>
+
-
        <li><a href="">Team</a></li>
+
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<li><a href="">Fun</a></li>
+
-
  </ul>
+
   </li>  
   </li>  
<li><a href="">PROJECT</a>
<li><a href="">PROJECT</a>
<ul>  
<ul>  
-
<li><a href="">Overview</a></li>  
+
<li><a href="https://2014.igem.org/Team:BostonU/Chimera">Overview</a></li>
 +
<li><a href="https://2014.igem.org/Team:BostonU/Encoder">Priority Encoder</a></li>
 +
<li><a href="https://2014.igem.org/Team:BostonU/MoClo">MoClo Assembly Method</a></li>
 +
                        <li><a href="https://2014.igem.org/Team:BostonU/Backbones">Low Copy Backbones</a></li>
 +
<li><a href="https://2014.igem.org/Team:BostonU/ProjectTandemPromoters">Tandem Promoters</a></li>
 +
      <li><a href="https://2014.igem.org/Team:BostonU/FusionProteins">Fusion Proteins</a></li>
 +
      <li><a href="https://2014.igem.org/Team:BostonU/Repressors">Repressor Proteins</a></li>
 +
            <li><a href="https://2014.igem.org/Team:BostonU/Multiplexing">Multiplexing</a></li>
 +
<li><a href="https://2014.igem.org/Team:BostonU/Software">BioDesign Automation Tools</a></li>
 +
            <li><a href="https://2014.igem.org/Team:BostonU/Future">Future Work</a></li>
 +
 
  </ul>
  </ul>
</li>  
</li>  
<li><a href="">ACHIEVEMENTS</a>
<li><a href="">ACHIEVEMENTS</a>
<ul>
<ul>
-
        <li><a href="">Data Collected</a></li>
+
        <li><a href="https://2014.igem.org/Team:BostonU/Data">Data Collected</a></li>
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<li><a href="">Parts Submitted</a></li>
+
<li><a href="https://2014.igem.org/Team:BostonU/Parts">Parts Submitted</a></li>
-
             <li><a href="">Workflow</a></li>
+
             <li><a href="https://2014.igem.org/Team:BostonU/Workflow">Chimera Workflow</a></li>
-
             <li><a href="">Medal Fulfillment</a></li>
+
             <li><a href="https://2014.igem.org/Team:BostonU/ChimeraExample">Chimera Example</a></li>
 +
            <li><a href="https://2014.igem.org/Team:BostonU/Medals">Medal Fulfillment</a></li>
 +
 
  </ul>
  </ul>
   </li>
   </li>
<li><a href="">NOTEBOOK</a>  
<li><a href="">NOTEBOOK</a>  
  <ul>  
  <ul>  
-
       <li><a href="">Training</a></li>  
+
       <li><a href="https://2014.igem.org/Team:BostonU/Training">Training</a></li>  
-
<li><a href="">Protocols</a></li>  
+
<li><a href="https://2014.igem.org/Team:BostonU/Protocols">Protocols</a></li>
 +
                        <li><a href="https://2014.igem.org/Team:BostonU/BackbonesNotebook">Backbones</a></li>
 +
                        <li><a href="https://2014.igem.org/Team:BostonU/TandemPromoters">Tandem Promoters and Repressors</a></li>
 +
                        <li><a href="https://2014.igem.org/Team:BostonU/FusionProteinsNotebook">Fusion Proteins</a></li>
  </ul>
  </ul>
   </li>
   </li>
<li><a href="">CONSIDERATIONS</a>
<li><a href="">CONSIDERATIONS</a>
     <ul>  
     <ul>  
-
<li><a href="">NEGEM</a></li>  
+
<li><a href="https://2014.igem.org/Team:BostonU/Collaborations">Collaborations</a></li>
-
            <li><a href="">Human Practices</a></li>  
+
<li><a href="https://2014.igem.org/Team:BostonU/Measurement">Measurement Track</a></li>
 +
<li><a href="https://2014.igem.org/Team:BostonU/Safety">Safety</a></li>
 +
<li><a href="https://2014.igem.org/Team:BostonU/Interlab">Interlab Study</a></li>
 +
<li><a href="https://2014.igem.org/Team:BostonU/NEGEM">NEGEM</a></li>  
 +
<li><a href="https://2014.igem.org/Team:BostonU/HumanPractices">Policy and Practices</a></li>  
  </ul>  
  </ul>  
-
<li><a href="">ACKNOWLEDGEMENTS</a>
+
<li><a href="https://2014.igem.org/Team:BostonU/Acknowledgements">ACKNOWLEDGEMENTS</a>
-
      <ul>
+
-
<li><a href="">Collaborations</a></li>
+
-
            <li><a href="">Acknowledgements</a></li>
+
-
</ul>  
+
   </li>
   </li>
</ul>
</ul>
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    <header1>chimera -
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<header1>Chimera</header1><h3>an optimized characterization workflow for synthetic biology</h3>
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<maincontent><br>
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    <header3>an optimized synthetic biology workflow</header3><br>
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         <th colspan="2" scope="col"><img src="https://static.igem.org/mediawiki/2014/e/ea/Workflow_bu14.png" width="525" height="317" alt="Workflow" style="float:right">Currently in synthetic biology, the creation of novel genetic circuits revolves around a familiar design-build-test cycle. As an increasing number of laboratories become involved in designing newer and more sophisticated constructs, the lack of standardization in production and characterization inhibits workflow efficiency and, by extension, growth of the field. The 2014 Boston University iGEM team seeks to employ a formalized and optimized workflow supported by new bio-design automation applications, with the aim of benefiting synthetic biologists seeking to more efficiently design, build, and characterize complex constructs.
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<h3>Abstract </h3>
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          Advancements in bio-design automation (or BDA) have allowed for the implementation of a variety of software and automation tools that help improve the design-build-test efficiency in a synthetic biology laboratory. We will take a novel approach to the design-build-test cycle by using software tools to formalize our workflows, thus making us one of the first BDA iGEM teams. Using basic parts from the <a href="http://cidarlab.org/" target="_blank">CIDAR</a> MoClo library (built by the <a href="https://2012.igem.org/Team:BostonU" target="_blank">2012</a> and <a href="https://2013.igem.org/Team:BostonU" target="_blank">2013</a> BU iGEM teams), we will build complex constructs using our formalized workflow, in addition to providing comprehensive characterization data for all new parts and improving data for existing parts in the <a href="http://parts.igem.org/Main_Page" target="_blank">Registry of Standard Biological Parts</a>. <br><br>
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<strong>The Joy of Cloning: Chimera, a Recipe for Integrating Computational Tools with Experimental Protocols </strong><br>
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          Our BDA approach will include utilizing various software tools throughout the design-build-test cycle in our wet lab work, including Eugene, Raven, and the TASBE flow cytometry tool.
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If BU can clone it, so can you! With a pinch of wet lab work and a dash of computational tools, we have developed a new recipe called <a href="https://2014.igem.org/Team:BostonU/Workflow">Chimera</a> that will help fellow synthetic biology cloners in the creation of their genetic devices! Chimera utilizes <a href="https://2014.igem.org/Team:BostonU/Software">bio-design automation software tools</a> with experimental protocols and builds upon a thoroughly characterized library of <a href="https://2014.igem.org/Team:BostonU/MoClo">MoClo</a> parts. This recipe, or workflow, integrates software tools to reduce human error and to structure the way device designs are chosen, assembled, and tested. To demonstrate that this workflow can be used by any level of cloner (beginner, intermediate, and advanced), we will highlight how we used Chimera to create:<br>
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<p class="tab"><li> individual genetic parts (namely <a href="https://2014.igem.org/Team:BostonU/ProjectTandemPromoters">tandem promoters</a>, <a href="https://2014.igem.org/Team:BostonU/FusionProteins">fusion proteins</a>, and <a href="https://2014.igem.org/Team:BostonU/Backbones">different backbones</a>), </p>
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          The design of our genetic devices will be facilitated by <a href="http://eugenecad.org/" target="_blank">Eugene</a>, a language specifically designed for the description of genetic networks. Eugene allows for a very efficient design process for new parts by providing an exhaustive list of possible transcriptional units that can be made with available genetic parts, while following a set of rules to ensure the viability of the final designs. <br><br>
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<p class="tab"><li> transcriptional units assembled from individual parts (with both new and previously made MoClo parts), and </p>
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          The building process will be facilitated by <a href="http://cidarlab.org/raven/" target="_blank">Raven</a>, a web-based tool that generates an assembly plan for genetic devices. Our team plans to build devices using the MoClo method employed by previous BU iGEM teams, in addition to multiplexing in order to build many variations on one design in an efficient one-pot reaction. <br><br>
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<p class="tab"><li> a complex genetic device (our goal is a <a href="https://2014.igem.org/Team:BostonU/Encoder">priority encoder</a>).</p>
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          We will use flow cytometry in conjunction with the <a href="https://synbiotools.bbn.com/" target="_blank">TASBE Tools</a> to test the functionality of new constructs and enhance the documentation available for existing parts in the Registry. Additionally, we will contribute several new parts and their characterization data to the Registry including hybrid promoters, fusion proteins, and a variety of new vectors.&nbsp;</th>
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<br><br><strong><a href="https://2014.igem.org/Team:BostonU/Chimera">Click here to explore our project!</a></strong></td></tr></table>
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t,n=x._data(this),r=n[e+"queue"],i=n[e+"queueHooks"],o=x.timers,a=r?r.length:0;for(n.finish=!0,x.queue(this,e,[]),i&&i.stop&&i.stop.call(this,!0),t=o.length;t--;)o[t].elem===this&&o[t].queue===e&&(o[t].anim.stop(!0),o.splice(t,1));for(t=0;a>t;t++)r[t]&&r[t].finish&&r[t].finish.call(this);delete n.finish})}});function ir(e,t){var n,r={height:e},i=0;for(t=t?1:0;4>i;i+=2-t)n=Zt[i],r["margin"+n]=r["padding"+n]=e;return t&&(r.opacity=r.width=e),r}x.each({slideDown:ir("show"),slideUp:ir("hide"),slideToggle:ir("toggle"),fadeIn:{opacity:"show"},fadeOut:{opacity:"hide"},fadeToggle:{opacity:"toggle"}},function(e,t){x.fn[e]=function(e,n,r){return this.animate(t,e,n,r)}}),x.speed=function(e,t,n){var r=e&&"object"==typeof e?x.extend({},e):{complete:n||!n&&t||x.isFunction(e)&&e,duration:e,easing:n&&t||t&&!x.isFunction(t)&&t};return r.duration=x.fx.off?0:"number"==typeof r.duration?r.duration:r.duration in x.fx.speeds?x.fx.speeds[r.duration]:x.fx.speeds._default,(null==r.queue||r.queue===!0)&&(r.queue="fx"),r.old=r.complete,r.complete=function(){x.isFunction(r.old)&&r.old.call(this),r.queue&&x.dequeue(this,r.queue)},r},x.easing={linear:function(e){return e},swing:function(e){return.5-Math.cos(e*Math.PI)/2}},x.timers=[],x.fx=rr.prototype.init,x.fx.tick=function(){var e,n=x.timers,r=0;for(Xn=x.now();n.length>r;r++)e=n[r],e()||n[r]!==e||n.splice(r--,1);n.length||x.fx.stop(),Xn=t},x.fx.timer=function(e){e()&&x.timers.push(e)&&x.fx.start()},x.fx.interval=13,x.fx.start=function(){Un||(Un=setInterval(x.fx.tick,x.fx.interval))},x.fx.stop=function(){clearInterval(Un),Un=null},x.fx.speeds={slow:600,fast:200,_default:400},x.fx.step={},x.expr&&x.expr.filters&&(x.expr.filters.animated=function(e){return x.grep(x.timers,function(t){return e===t.elem}).length}),x.fn.offset=function(e){if(arguments.length)return e===t?this:this.each(function(t){x.offset.setOffset(this,e,t)});var n,r,o={top:0,left:0},a=this[0],s=a&&a.ownerDocument;if(s)return n=s.documentElement,x.contains(n,a)?(typeof a.getBoundingClientRect!==i&&(o=a.getBoundingClientRect()),r=or(s),{top:o.top+(r.pageYOffset||n.scrollTop)-(n.clientTop||0),left:o.left+(r.pageXOffset||n.scrollLeft)-(n.clientLeft||0)}):o},x.offset={setOffset:function(e,t,n){var r=x.css(e,"position");"static"===r&&(e.style.position="relative");var i=x(e),o=i.offset(),a=x.css(e,"top"),s=x.css(e,"left"),l=("absolute"===r||"fixed"===r)&&x.inArray("auto",[a,s])>-1,u={},c={},p,f;l?(c=i.position(),p=c.top,f=c.left):(p=parseFloat(a)||0,f=parseFloat(s)||0),x.isFunction(t)&&(t=t.call(e,n,o)),null!=t.top&&(u.top=t.top-o.top+p),null!=t.left&&(u.left=t.left-o.left+f),"using"in t?t.using.call(e,u):i.css(u)}},x.fn.extend({position:function(){if(this[0]){var e,t,n={top:0,left:0},r=this[0];return"fixed"===x.css(r,"position")?t=r.getBoundingClientRect():(e=this.offsetParent(),t=this.offset(),x.nodeName(e[0],"html")||(n=e.offset()),n.top+=x.css(e[0],"borderTopWidth",!0),n.left+=x.css(e[0],"borderLeftWidth",!0)),{top:t.top-n.top-x.css(r,"marginTop",!0),left:t.left-n.left-x.css(r,"marginLeft",!0)}}},offsetParent:function(){return this.map(function(){var e=this.offsetParent||s;while(e&&!x.nodeName(e,"html")&&"static"===x.css(e,"position"))e=e.offsetParent;return e||s})}}),x.each({scrollLeft:"pageXOffset",scrollTop:"pageYOffset"},function(e,n){var r=/Y/.test(n);x.fn[e]=function(i){return x.access(this,function(e,i,o){var a=or(e);return o===t?a?n in a?a[n]:a.document.documentElement[i]:e[i]:(a?a.scrollTo(r?x(a).scrollLeft():o,r?o:x(a).scrollTop()):e[i]=o,t)},e,i,arguments.length,null)}});function or(e){return x.isWindow(e)?e:9===e.nodeType?e.defaultView||e.parentWindow:!1}x.each({Height:"height",Width:"width"},function(e,n){x.each({padding:"inner"+e,content:n,"":"outer"+e},function(r,i){x.fn[i]=function(i,o){var a=arguments.length&&(r||"boolean"!=typeof i),s=r||(i===!0||o===!0?"margin":"border");return x.access(this,function(n,r,i){var o;return x.isWindow(n)?n.document.documentElement["client"+e]:9===n.nodeType?(o=n.documentElement,Math.max(n.body["scroll"+e],o["scroll"+e],n.body["offset"+e],o["offset"+e],o["client"+e])):i===t?x.css(n,r,s):x.style(n,r,i,s)},n,a?i:t,a,null)}})}),x.fn.size=function(){return this.length},x.fn.andSelf=x.fn.addBack,"object"==typeof module&&module&&"object"==typeof module.exports?module.exports=x:(e.jQuery=e.$=x,"function"==typeof define&&define.amd&&define("jquery",[],function(){return x}))})(window);
+
-
</script>
+
-
 
+
-
<!--jquery.event.move-->
+
-
<script type='text/javascript'>
+
-
(function (module) {
+
-
if (typeof define === 'function' && define.amd) {
+
-
// AMD. Register as an anonymous module.
+
-
define(['jquery'], module);
+
-
} else {
+
-
// Browser globals
+
-
module(jQuery);
+
-
}
+
-
})(function(jQuery, undefined){
+
-
 
+
-
var // Number of pixels a pressed pointer travels before movestart
+
-
    // event is fired.
+
-
    threshold = 6,
+
-
 
+
-
    add = jQuery.event.add,
+
-
 
+
-
    remove = jQuery.event.remove,
+
-
 
+
-
    // Just sugar, so we can have arguments in the same order as
+
-
    // add and remove.
+
-
    trigger = function(node, type, data) {
+
-
    jQuery.event.trigger(type, data, node);
+
-
    },
+
-
 
+
-
    // Shim for requestAnimationFrame, falling back to timer. See:
+
-
    // see http://paulirish.com/2011/requestanimationframe-for-smart-animating/
+
-
    requestFrame = (function(){
+
-
    return (
+
-
    window.requestAnimationFrame ||
+
-
    window.webkitRequestAnimationFrame ||
+
-
    window.mozRequestAnimationFrame ||
+
-
    window.oRequestAnimationFrame ||
+
-
    window.msRequestAnimationFrame ||
+
-
    function(fn, element){
+
-
    return window.setTimeout(function(){
+
-
    fn();
+
-
    }, 25);
+
-
    }
+
-
    );
+
-
    })(),
+
-
 
+
-
    ignoreTags = {
+
-
    textarea: true,
+
-
    input: true,
+
-
    select: true,
+
-
    button: true
+
-
    },
+
-
 
+
-
    mouseevents = {
+
-
    move: 'mousemove',
+
-
    cancel: 'mouseup dragstart',
+
-
    end: 'mouseup'
+
-
    },
+
-
 
+
-
    touchevents = {
+
-
    move: 'touchmove',
+
-
    cancel: 'touchend',
+
-
    end: 'touchend'
+
-
    };
+
-
 
+
-
 
+
-
// Constructors
+
-
 
+
-
function Timer(fn){
+
-
var callback = fn,
+
-
    active = false,
+
-
    running = false;
+
-
 
+
-
function trigger(time) {
+
-
if (active){
+
-
callback();
+
-
requestFrame(trigger);
+
-
running = true;
+
-
active = false;
+
-
}
+
-
else {
+
-
running = false;
+
-
}
+
-
}
+
-
 
+
-
this.kick = function(fn) {
+
-
active = true;
+
-
if (!running) { trigger(); }
+
-
};
+
-
 
+
-
this.end = function(fn) {
+
-
var cb = callback;
+
-
 
+
-
if (!fn) { return; }
+
-
 
+
-
// If the timer is not running, simply call the end callback.
+
-
if (!running) {
+
-
fn();
+
-
}
+
-
// If the timer is running, and has been kicked lately, then
+
-
// queue up the current callback and the end callback, otherwise
+
-
// just the end callback.
+
-
else {
+
-
callback = active ?
+
-
function(){ cb(); fn(); } :
+
-
fn ;
+
-
 
+
-
active = true;
+
-
}
+
-
};
+
-
}
+
-
 
+
-
 
+
-
// Functions
+
-
 
+
-
function returnTrue() {
+
-
return true;
+
-
}
+
-
 
+
-
function returnFalse() {
+
-
return false;
+
-
}
+
-
 
+
-
function preventDefault(e) {
+
-
e.preventDefault();
+
-
}
+
-
 
+
-
function preventIgnoreTags(e) {
+
-
// Don't prevent interaction with form elements.
+
-
if (ignoreTags[ e.target.tagName.toLowerCase() ]) { return; }
+
-
 
+
-
e.preventDefault();
+
-
}
+
-
 
+
-
function isLeftButton(e) {
+
-
// Ignore mousedowns on any button other than the left (or primary)
+
-
// mouse button, or when a modifier key is pressed.
+
-
return (e.which === 1 && !e.ctrlKey && !e.altKey);
+
-
}
+
-
 
+
-
function identifiedTouch(touchList, id) {
+
-
var i, l;
+
-
 
+
-
if (touchList.identifiedTouch) {
+
-
return touchList.identifiedTouch(id);
+
-
}
+
-
 
+
-
// touchList.identifiedTouch() does not exist in
+
-
// webkit yet… we must do the search ourselves...
+
-
 
+
-
i = -1;
+
-
l = touchList.length;
+
-
 
+
-
while (++i < l) {
+
-
if (touchList[i].identifier === id) {
+
-
return touchList[i];
+
-
}
+
-
}
+
-
}
+
-
 
+
-
function changedTouch(e, event) {
+
-
var touch = identifiedTouch(e.changedTouches, event.identifier);
+
-
 
+
-
// This isn't the touch you're looking for.
+
-
if (!touch) { return; }
+
-
 
+
-
// Chrome Android (at least) includes touches that have not
+
-
// changed in e.changedTouches. That's a bit annoying. Check
+
-
// that this touch has changed.
+
-
if (touch.pageX === event.pageX && touch.pageY === event.pageY) { return; }
+
-
 
+
-
return touch;
+
-
}
+
-
 
+
-
 
+
-
// Handlers that decide when the first movestart is triggered
+
-
 
+
-
function mousedown(e){
+
-
var data;
+
-
 
+
-
if (!isLeftButton(e)) { return; }
+
-
 
+
-
data = {
+
-
target: e.target,
+
-
startX: e.pageX,
+
-
startY: e.pageY,
+
-
timeStamp: e.timeStamp
+
-
};
+
-
 
+
-
add(document, mouseevents.move, mousemove, data);
+
-
add(document, mouseevents.cancel, mouseend, data);
+
-
}
+
-
 
+
-
function mousemove(e){
+
-
var data = e.data;
+
-
 
+
-
checkThreshold(e, data, e, removeMouse);
+
-
}
+
-
 
+
-
function mouseend(e) {
+
-
removeMouse();
+
-
}
+
-
 
+
-
function removeMouse() {
+
-
remove(document, mouseevents.move, mousemove);
+
-
remove(document, mouseevents.cancel, mouseend);
+
-
}
+
-
 
+
-
function touchstart(e) {
+
-
var touch, template;
+
-
 
+
-
// Don't get in the way of interaction with form elements.
+
-
if (ignoreTags[ e.target.tagName.toLowerCase() ]) { return; }
+
-
 
+
-
touch = e.changedTouches[0];
+
-
 
+
-
// iOS live updates the touch objects whereas Android gives us copies.
+
-
// That means we can't trust the touchstart object to stay the same,
+
-
// so we must copy the data. This object acts as a template for
+
-
// movestart, move and moveend event objects.
+
-
template = {
+
-
target: touch.target,
+
-
startX: touch.pageX,
+
-
startY: touch.pageY,
+
-
timeStamp: e.timeStamp,
+
-
identifier: touch.identifier
+
-
};
+
-
 
+
-
// Use the touch identifier as a namespace, so that we can later
+
-
// remove handlers pertaining only to this touch.
+
-
add(document, touchevents.move + '.' + touch.identifier, touchmove, template);
+
-
add(document, touchevents.cancel + '.' + touch.identifier, touchend, template);
+
-
}
+
-
 
+
-
function touchmove(e){
+
-
var data = e.data,
+
-
    touch = changedTouch(e, data);
+
-
 
+
-
if (!touch) { return; }
+
-
 
+
-
checkThreshold(e, data, touch, removeTouch);
+
-
}
+
-
 
+
-
function touchend(e) {
+
-
var template = e.data,
+
-
    touch = identifiedTouch(e.changedTouches, template.identifier);
+
-
 
+
-
if (!touch) { return; }
+
-
 
+
-
removeTouch(template.identifier);
+
-
}
+
-
 
+
-
function removeTouch(identifier) {
+
-
remove(document, '.' + identifier, touchmove);
+
-
remove(document, '.' + identifier, touchend);
+
-
}
+
-
 
+
-
 
+
-
// Logic for deciding when to trigger a movestart.
+
-
 
+
-
function checkThreshold(e, template, touch, fn) {
+
-
var distX = touch.pageX - template.startX,
+
-
    distY = touch.pageY - template.startY;
+
-
 
+
-
// Do nothing if the threshold has not been crossed.
+
-
if ((distX * distX) + (distY * distY) < (threshold * threshold)) { return; }
+
-
 
+
-
triggerStart(e, template, touch, distX, distY, fn);
+
-
}
+
-
 
+
-
function handled() {
+
-
// this._handled should return false once, and after return true.
+
-
this._handled = returnTrue;
+
-
return false;
+
-
}
+
-
 
+
-
function flagAsHandled(e) {
+
-
e._handled();
+
-
}
+
-
 
+
-
function triggerStart(e, template, touch, distX, distY, fn) {
+
-
var node = template.target,
+
-
    touches, time;
+
-
 
+
-
touches = e.targetTouches;
+
-
time = e.timeStamp - template.timeStamp;
+
-
 
+
-
// Create a movestart object with some special properties that
+
-
// are passed only to the movestart handlers.
+
-
template.type = 'movestart';
+
-
template.distX = distX;
+
-
template.distY = distY;
+
-
template.deltaX = distX;
+
-
template.deltaY = distY;
+
-
template.pageX = touch.pageX;
+
-
template.pageY = touch.pageY;
+
-
template.velocityX = distX / time;
+
-
template.velocityY = distY / time;
+
-
template.targetTouches = touches;
+
-
template.finger = touches ?
+
-
touches.length :
+
-
1 ;
+
-
 
+
-
// The _handled method is fired to tell the default movestart
+
-
// handler that one of the move events is bound.
+
-
template._handled = handled;
+
-
 
+
-
// Pass the touchmove event so it can be prevented if or when
+
-
// movestart is handled.
+
-
template._preventTouchmoveDefault = function() {
+
-
e.preventDefault();
+
-
};
+
-
 
+
-
// Trigger the movestart event.
+
-
trigger(template.target, template);
+
-
 
+
-
// Unbind handlers that tracked the touch or mouse up till now.
+
-
fn(template.identifier);
+
-
}
+
-
 
+
-
 
+
-
// Handlers that control what happens following a movestart
+
-
 
+
-
function activeMousemove(e) {
+
-
var timer = e.data.timer;
+
-
 
+
-
e.data.touch = e;
+
-
e.data.timeStamp = e.timeStamp;
+
-
timer.kick();
+
-
}
+
-
 
+
-
function activeMouseend(e) {
+
-
var event = e.data.event,
+
-
    timer = e.data.timer;
+
-
 
+
-
removeActiveMouse();
+
-
 
+
-
endEvent(event, timer, function() {
+
-
// Unbind the click suppressor, waiting until after mouseup
+
-
// has been handled.
+
-
setTimeout(function(){
+
-
remove(event.target, 'click', returnFalse);
+
-
}, 0);
+
-
});
+
-
}
+
-
 
+
-
function removeActiveMouse(event) {
+
-
remove(document, mouseevents.move, activeMousemove);
+
-
remove(document, mouseevents.end, activeMouseend);
+
-
}
+
-
 
+
-
function activeTouchmove(e) {
+
-
var event = e.data.event,
+
-
    timer = e.data.timer,
+
-
    touch = changedTouch(e, event);
+
-
 
+
-
if (!touch) { return; }
+
-
 
+
-
// Stop the interface from gesturing
+
-
e.preventDefault();
+
-
 
+
-
event.targetTouches = e.targetTouches;
+
-
e.data.touch = touch;
+
-
e.data.timeStamp = e.timeStamp;
+
-
timer.kick();
+
-
}
+
-
 
+
-
function activeTouchend(e) {
+
-
var event = e.data.event,
+
-
    timer = e.data.timer,
+
-
    touch = identifiedTouch(e.changedTouches, event.identifier);
+
-
 
+
-
// This isn't the touch you're looking for.
+
-
if (!touch) { return; }
+
-
 
+
-
removeActiveTouch(event);
+
-
endEvent(event, timer);
+
-
}
+
-
 
+
-
function removeActiveTouch(event) {
+
-
remove(document, '.' + event.identifier, activeTouchmove);
+
-
remove(document, '.' + event.identifier, activeTouchend);
+
-
}
+
-
 
+
-
 
+
-
// Logic for triggering move and moveend events
+
-
 
+
-
function updateEvent(event, touch, timeStamp, timer) {
+
-
var time = timeStamp - event.timeStamp;
+
-
 
+
-
event.type = 'move';
+
-
event.distX =  touch.pageX - event.startX;
+
-
event.distY =  touch.pageY - event.startY;
+
-
event.deltaX = touch.pageX - event.pageX;
+
-
event.deltaY = touch.pageY - event.pageY;
+
-
 
+
-
// Average the velocity of the last few events using a decay
+
-
// curve to even out spurious jumps in values.
+
-
event.velocityX = 0.3 * event.velocityX + 0.7 * event.deltaX / time;
+
-
event.velocityY = 0.3 * event.velocityY + 0.7 * event.deltaY / time;
+
-
event.pageX =  touch.pageX;
+
-
event.pageY =  touch.pageY;
+
-
}
+
-
 
+
-
function endEvent(event, timer, fn) {
+
-
timer.end(function(){
+
-
event.type = 'moveend';
+
-
 
+
-
trigger(event.target, event);
+
-
 
+
-
return fn && fn();
+
-
});
+
-
}
+
-
 
+
-
 
+
-
// jQuery special event definition
+
-
 
+
-
function setup(data, namespaces, eventHandle) {
+
-
// Stop the node from being dragged
+
-
//add(this, 'dragstart.move drag.move', preventDefault);
+
-
 
+
-
// Prevent text selection and touch interface scrolling
+
-
//add(this, 'mousedown.move', preventIgnoreTags);
+
-
 
+
-
// Tell movestart default handler that we've handled this
+
-
add(this, 'movestart.move', flagAsHandled);
+
-
 
+
-
// Don't bind to the DOM. For speed.
+
-
return true;
+
-
}
+
-
 
+
-
function teardown(namespaces) {
+
-
remove(this, 'dragstart drag', preventDefault);
+
-
remove(this, 'mousedown touchstart', preventIgnoreTags);
+
-
remove(this, 'movestart', flagAsHandled);
+
-
 
+
-
// Don't bind to the DOM. For speed.
+
-
return true;
+
-
}
+
-
 
+
-
function addMethod(handleObj) {
+
-
// We're not interested in preventing defaults for handlers that
+
-
// come from internal move or moveend bindings
+
-
if (handleObj.namespace === "move" || handleObj.namespace === "moveend") {
+
-
return;
+
-
}
+
-
 
+
-
// Stop the node from being dragged
+
-
add(this, 'dragstart.' + handleObj.guid + ' drag.' + handleObj.guid, preventDefault, undefined, handleObj.selector);
+
-
 
+
-
// Prevent text selection and touch interface scrolling
+
-
add(this, 'mousedown.' + handleObj.guid, preventIgnoreTags, undefined, handleObj.selector);
+
-
}
+
-
 
+
-
function removeMethod(handleObj) {
+
-
if (handleObj.namespace === "move" || handleObj.namespace === "moveend") {
+
-
return;
+
-
}
+
-
 
+
-
remove(this, 'dragstart.' + handleObj.guid + ' drag.' + handleObj.guid);
+
-
remove(this, 'mousedown.' + handleObj.guid);
+
-
}
+
-
 
+
-
jQuery.event.special.movestart = {
+
-
setup: setup,
+
-
teardown: teardown,
+
-
add: addMethod,
+
-
remove: removeMethod,
+
-
 
+
-
_default: function(e) {
+
-
var event, data;
+
-
 
+
-
// If no move events were bound to any ancestors of this
+
-
// target, high tail it out of here.
+
-
if (!e._handled()) { return; }
+
-
 
+
-
function update(time) {
+
-
updateEvent(event, data.touch, data.timeStamp);
+
-
trigger(e.target, event);
+
-
}
+
-
 
+
-
event = {
+
-
target: e.target,
+
-
startX: e.startX,
+
-
startY: e.startY,
+
-
pageX: e.pageX,
+
-
pageY: e.pageY,
+
-
distX: e.distX,
+
-
distY: e.distY,
+
-
deltaX: e.deltaX,
+
-
deltaY: e.deltaY,
+
-
velocityX: e.velocityX,
+
-
velocityY: e.velocityY,
+
-
timeStamp: e.timeStamp,
+
-
identifier: e.identifier,
+
-
targetTouches: e.targetTouches,
+
-
finger: e.finger
+
-
};
+
-
 
+
-
data = {
+
-
event: event,
+
-
timer: new Timer(update),
+
-
touch: undefined,
+
-
timeStamp: undefined
+
-
};
+
-
 
+
-
if (e.identifier === undefined) {
+
-
// We're dealing with a mouse
+
-
// Stop clicks from propagating during a move
+
-
add(e.target, 'click', returnFalse);
+
-
add(document, mouseevents.move, activeMousemove, data);
+
-
add(document, mouseevents.end, activeMouseend, data);
+
-
}
+
-
else {
+
-
// We're dealing with a touch. Stop touchmove doing
+
-
// anything defaulty.
+
-
e._preventTouchmoveDefault();
+
-
add(document, touchevents.move + '.' + e.identifier, activeTouchmove, data);
+
-
add(document, touchevents.end + '.' + e.identifier, activeTouchend, data);
+
-
}
+
-
}
+
-
};
+
-
 
+
-
jQuery.event.special.move = {
+
-
setup: function() {
+
-
// Bind a noop to movestart. Why? It's the movestart
+
-
// setup that decides whether other move events are fired.
+
-
add(this, 'movestart.move', jQuery.noop);
+
-
},
+
-
 
+
-
teardown: function() {
+
-
remove(this, 'movestart.move', jQuery.noop);
+
-
}
+
-
};
+
-
 
+
-
jQuery.event.special.moveend = {
+
-
setup: function() {
+
-
// Bind a noop to movestart. Why? It's the movestart
+
-
// setup that decides whether other move events are fired.
+
-
add(this, 'movestart.moveend', jQuery.noop);
+
-
},
+
-
 
+
-
teardown: function() {
+
-
remove(this, 'movestart.moveend', jQuery.noop);
+
-
}
+
-
};
+
-
 
+
-
add(document, 'mousedown.move', mousedown);
+
-
add(document, 'touchstart.move', touchstart);
+
-
 
+
-
// Make jQuery copy touch event properties over to the jQuery event
+
-
// object, if they are not already listed. But only do the ones we
+
-
// really need. IE7/8 do not have Array#indexOf(), but nor do they
+
-
// have touch events, so let's assume we can ignore them.
+
-
if (typeof Array.prototype.indexOf === 'function') {
+
-
(function(jQuery, undefined){
+
-
var props = ["changedTouches", "targetTouches"],
+
-
    l = props.length;
+
-
 
+
-
while (l--) {
+
-
if (jQuery.event.props.indexOf(props[l]) === -1) {
+
-
jQuery.event.props.push(props[l]);
+
-
}
+
-
}
+
-
})(jQuery);
+
-
};
+
-
});
+
-
</script>
+
-
 
+
-
<!--jquery.event.swipe-->
+
-
<script type='text/javascript'>
+
-
// jQuery.event.swipe
+
-
// 0.5
+
-
// Stephen Band
+
-
 
+
-
// Dependencies
+
-
// jQuery.event.move 1.2
+
-
 
+
-
// One of swipeleft, swiperight, swipeup or swipedown is triggered on
+
-
// moveend, when the move has covered a threshold ratio of the dimension
+
-
// of the target node, or has gone really fast. Threshold and velocity
+
-
// sensitivity changed with:
+
-
//
+
-
// jQuery.event.special.swipe.settings.threshold
+
-
// jQuery.event.special.swipe.settings.sensitivity
+
-
 
+
-
(function (module) {
+
-
if (typeof define === 'function' && define.amd) {
+
-
// AMD. Register as an anonymous module.
+
-
define(['jquery'], module);
+
-
} else {
+
-
// Browser globals
+
-
module(jQuery);
+
-
}
+
-
})(function(jQuery, undefined){
+
-
var add = jQuery.event.add,
+
-
 
+
-
    remove = jQuery.event.remove,
+
-
 
+
-
    // Just sugar, so we can have arguments in the same order as
+
-
    // add and remove.
+
-
    trigger = function(node, type, data) {
+
-
    jQuery.event.trigger(type, data, node);
+
-
    },
+
-
 
+
-
    settings = {
+
-
    // Ratio of distance over target finger must travel to be
+
-
    // considered a swipe.
+
-
    threshold: 0.4,
+
-
    // Faster fingers can travel shorter distances to be considered
+
-
    // swipes. 'sensitivity' controls how much. Bigger is shorter.
+
-
    sensitivity: 6
+
-
    };
+
-
 
+
-
function moveend(e) {
+
-
var w, h, event;
+
-
 
+
-
w = e.currentTarget.offsetWidth;
+
-
h = e.currentTarget.offsetHeight;
+
-
 
+
-
// Copy over some useful properties from the move event
+
-
event = {
+
-
distX: e.distX,
+
-
distY: e.distY,
+
-
velocityX: e.velocityX,
+
-
velocityY: e.velocityY,
+
-
finger: e.finger
+
-
};
+
-
 
+
-
// Find out which of the four directions was swiped
+
-
if (e.distX > e.distY) {
+
-
if (e.distX > -e.distY) {
+
-
if (e.distX/w > settings.threshold || e.velocityX * e.distX/w * settings.sensitivity > 1) {
+
-
event.type = 'swiperight';
+
-
trigger(e.currentTarget, event);
+
-
}
+
-
}
+
-
else {
+
-
if (-e.distY/h > settings.threshold || e.velocityY * e.distY/w * settings.sensitivity > 1) {
+
-
event.type = 'swipeup';
+
-
trigger(e.currentTarget, event);
+
-
}
+
-
}
+
-
}
+
-
else {
+
-
if (e.distX > -e.distY) {
+
-
if (e.distY/h > settings.threshold || e.velocityY * e.distY/w * settings.sensitivity > 1) {
+
-
event.type = 'swipedown';
+
-
trigger(e.currentTarget, event);
+
-
}
+
-
}
+
-
else {
+
-
if (-e.distX/w > settings.threshold || e.velocityX * e.distX/w * settings.sensitivity > 1) {
+
-
event.type = 'swipeleft';
+
-
trigger(e.currentTarget, event);
+
-
}
+
-
}
+
-
}
+
-
}
+
-
 
+
-
function getData(node) {
+
-
var data = jQuery.data(node, 'event_swipe');
+
-
 
+
-
if (!data) {
+
-
data = { count: 0 };
+
-
jQuery.data(node, 'event_swipe', data);
+
-
}
+
-
 
+
-
return data;
+
-
}
+
-
 
+
-
jQuery.event.special.swipe =
+
-
jQuery.event.special.swipeleft =
+
-
jQuery.event.special.swiperight =
+
-
jQuery.event.special.swipeup =
+
-
jQuery.event.special.swipedown = {
+
-
setup: function( data, namespaces, eventHandle ) {
+
-
var data = getData(this);
+
-
 
+
-
// If another swipe event is already setup, don't setup again.
+
-
if (data.count++ > 0) { return; }
+
-
 
+
-
add(this, 'moveend', moveend);
+
-
 
+
-
return true;
+
-
},
+
-
 
+
-
teardown: function() {
+
-
var data = getData(this);
+
-
 
+
-
// If another swipe event is still setup, don't teardown.
+
-
if (--data.count > 0) { return; }
+
-
 
+
-
remove(this, 'moveend', moveend);
+
-
 
+
-
return true;
+
-
},
+
-
 
+
-
settings: settings
+
-
};
+
-
});
+
-
</script>
+
-
 
+
-
<!--scrollto-->
+
-
<script type='text/javascript'>
+
-
/**
+
-
* Copyright (c) 2007-2014 Ariel Flesler - aflesler<a>gmail<d>com | http://flesler.blogspot.com
+
-
* Licensed under MIT
+
-
* @author Ariel Flesler
+
-
* @version 1.4.11
+
-
*/
+
-
;(function(a){if(typeof define==='function'&&define.amd){define(['jquery'],a)}else{a(jQuery)}}(function($){var j=$.scrollTo=function(a,b,c){return $(window).scrollTo(a,b,c)};j.defaults={axis:'xy',duration:parseFloat($.fn.jquery)>=1.3?0:1,limit:true};j.window=function(a){return $(window)._scrollable()};$.fn._scrollable=function(){return this.map(function(){var a=this,isWin=!a.nodeName||$.inArray(a.nodeName.toLowerCase(),['iframe','#document','html','body'])!=-1;if(!isWin)return a;var b=(a.contentWindow||a).document||a.ownerDocument||a;return/webkit/i.test(navigator.userAgent)||b.compatMode=='BackCompat'?b.body:b.documentElement})};$.fn.scrollTo=function(f,g,h){if(typeof g=='object'){h=g;g=0}if(typeof h=='function')h={onAfter:h};if(f=='max')f=9e9;h=$.extend({},j.defaults,h);g=g||h.duration;h.queue=h.queue&&h.axis.length>1;if(h.queue)g/=2;h.offset=both(h.offset);h.over=both(h.over);return this._scrollable().each(function(){if(f==null)return;var d=this,$elem=$(d),targ=f,toff,attr={},win=$elem.is('html,body');switch(typeof targ){case'number':case'string':if(/^([+-]=?)?\d+(\.\d+)?(px|%)?$/.test(targ)){targ=both(targ);break}targ=$(targ,this);if(!targ.length)return;case'object':if(targ.is||targ.style)toff=(targ=$(targ)).offset()}var e=$.isFunction(h.offset)&&h.offset(d,targ)||h.offset;$.each(h.axis.split(''),function(i,a){var b=a=='x'?'Left':'Top',pos=b.toLowerCase(),key='scroll'+b,old=d[key],max=j.max(d,a);if(toff){attr[key]=toff[pos]+(win?0:old-$elem.offset()[pos]);if(h.margin){attr[key]-=parseInt(targ.css('margin'+b))||0;attr[key]-=parseInt(targ.css('border'+b+'Width'))||0}attr[key]+=e[pos]||0;if(h.over[pos])attr[key]+=targ[a=='x'?'width':'height']()*h.over[pos]}else{var c=targ[pos];attr[key]=c.slice&&c.slice(-1)=='%'?parseFloat(c)/100*max:c}if(h.limit&&/^\d+$/.test(attr[key]))attr[key]=attr[key]<=0?0:Math.min(attr[key],max);if(!i&&h.queue){if(old!=attr[key])animate(h.onAfterFirst);delete attr[key]}});animate(h.onAfter);function animate(a){$elem.animate(attr,g,h.easing,a&&function(){a.call(this,targ,h)})}}).end()};j.max=function(a,b){var c=b=='x'?'Width':'Height',scroll='scroll'+c;if(!$(a).is('html,body'))return a[scroll]-$(a)[c.toLowerCase()]();var d='client'+c,html=a.ownerDocument.documentElement,body=a.ownerDocument.body;return Math.max(html[scroll],body[scroll])-Math.min(html[d],body[d])};function both(a){return $.isFunction(a)||typeof a=='object'?a:{top:a,left:a}};return j}));
+
-
</script>
+
-
 
+
-
<!--init-->
+
-
<script type='text/javascript'>
+
-
jQuery(function( $ ){
+
-
/**
+
-
* Demo binding and preparation, no need to read this part
+
-
*/
+
-
//borrowed from jQuery easing plugin
+
-
//http://gsgd.co.uk/sandbox/jquery.easing.php
+
-
$.easing.elasout = function(x, t, b, c, d) {
+
-
var s=1.70158;var p=0;var a=c;
+
-
if (t==0) return b;  if ((t/=d)==1) return b+c;  if (!p) p=d*.3;
+
-
if (a < Math.abs(c)) { a=c; var s=p/4; }
+
-
else var s = p/(2*Math.PI) * Math.asin (c/a);
+
-
return a*Math.pow(2,-10*t) * Math.sin( (t*d-s)*(2*Math.PI)/p ) + c + b;
+
-
};
+
-
$('a.back').click(function(){
+
-
$(this).parents('div.pane').scrollTo( 0, 800, { queue:true } );
+
-
$(this).parents('div.section').find('span.message').text( this.title );
+
-
return false;
+
-
});
+
-
//just for the example, to stop the click on the links.
+
-
$('ul.links').click(function(e){
+
-
e.preventDefault();
+
-
var link = e.target;
+
-
link.blur();
+
-
if( link.title )
+
-
$(this).parent().find('span.message').text(link.title);
+
-
});
+
-
+
-
// This one is important, many browsers don't reset scroll on refreshes
+
-
// Reset all scrollable panes to (0,0)
+
-
$('div.pane').scrollTo( 0 );
+
-
// Reset the screen to (0,0)
+
-
$.scrollTo( 0 );
+
-
+
-
// TOC, shows how to scroll the whole window
+
-
$('#toc a').click(function(){//$.scrollTo works EXACTLY the same way, but scrolls the whole screen
+
-
$.scrollTo( this.hash, 1500, { easing:'elasout' });
+
-
$(this.hash).find('span.message').text( this.title );
+
-
return false;
+
-
});
+
-
+
-
// Target examples bindings
+
-
var $paneTarget = $('#pane-target');
+
-
+
-
$('#relative-selector').click(function(){
+
-
$paneTarget.stop().scrollTo( 'li:eq(14)', 800 );
+
-
});
+
-
$('#jquery-object').click(function(){
+
-
var $target = $paneTarget.find('li:eq(14)');
+
-
$paneTarget.stop().scrollTo( $target , 800 );
+
-
});
+
-
$('#dom-element').click(function(){
+
-
var target = $paneTarget.find('ul').get(0).childNodes[20];
+
-
$paneTarget.stop().scrollTo( target, 800 );
+
-
});
+
-
$('#absolute-number').click(function(){
+
-
$paneTarget.stop().scrollTo( 150, 800 );
+
-
});
+
-
$('#absolute-number-hash').click(function(){
+
-
$paneTarget.stop().scrollTo( { top:800,left:700} , 800 );
+
-
});
+
-
$('#absolute-position').click(function(){
+
-
$paneTarget.stop().scrollTo( '520px', 800 );
+
-
});
+
-
$('#absolute-position-hash').click(function(){
+
-
$paneTarget.stop().scrollTo( {top:'110px',left:'290px'}, 800 );
+
-
});
+
-
$('#relative-position').click(function(){
+
-
$paneTarget.stop().scrollTo( '+=100', 500 );
+
-
});
+
-
$('#relative-position-hash').click(function(){
+
-
$paneTarget.stop().scrollTo( {top:'-=100px',left:'+=100'}, 500 );
+
-
});
+
-
+
-
$('#percentage-position').click(function(){
+
-
$paneTarget.stop().scrollTo( '50%', 800 );
+
-
});
+
-
+
-
// Options examples bindings, they will all scroll to the same place, with different options
+
-
function reset_o(){//before each animation, reset to (0,0), skip this.
+
-
$paneOptions.stop().stop();
+
-
$paneOptions[0].scrollLeft = $paneOptions[0].scrollTop = 0;
+
-
};
+
-
var $paneOptions = $('#pane-options');
+
-
+
-
$('#options-no').click(function(){
+
-
reset_o(); $paneOptions.scrollTo( 'li:eq(15)', 1000 );
+
-
});
+
-
$('#options-axis').click(function(){// only scroll horizontally
+
-
reset_o(); $paneOptions.scrollTo( 'li:eq(15)', 1000, { axis:'x' } );
+
-
});
+
-
$('#options-duration').click(function(){// it's the same as specifying it in the 2nd argument
+
-
reset_o(); $paneOptions.scrollTo( 'li:eq(15)', { duration: 3000 } );
+
-
});
+
-
$('#options-easing').click(function(){
+
-
reset_o(); $paneOptions.scrollTo( 'li:eq(15)', 2500, { easing:'elasout' } );
+
-
});
+
-
$('#options-margin').click(function(){//scroll to the "outer" position of the element
+
-
reset_o(); $paneOptions.scrollTo( 'li:eq(15)', 1000, { margin:true } );
+
-
});
+
-
$('#options-offset').click(function(){//same as { top:-50, left:-50 }
+
-
reset_o(); $paneOptions.scrollTo( 'li:eq(15)', 1000, { offset:-50 } );
+
-
});
+
-
$('#options-offset-hash').click(function(){
+
-
reset_o(); $paneOptions.scrollTo( 'li:eq(15)', 1000, { offset:{ top:-5,left:-30 } });
+
-
});
+
-
$('#options-offset-function').click(function(){
+
-
reset_o(); $paneOptions.scrollTo( 'li:eq(15)', 1000, {offset: function() { return {top:-30, left:-5}; }});
+
-
});
+
-
$('#options-over').click(function(){//same as { top:-50, left:-50 }
+
-
reset_o(); $paneOptions.scrollTo( 'li:eq(15)', 1000, { over:0.5 });
+
-
});
+
-
$('#options-over-hash').click(function(){
+
-
reset_o(); $paneOptions.scrollTo( 'li:eq(15)', 1000, { over:{ top:0.2, left:-0.5 } });
+
-
});
+
-
$('#options-queue').click(function(){//in this case, having 'axis' as 'xy' or 'yx' matters.
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Latest revision as of 03:24, 18 October 2014



Chimera

an optimized characterization workflow for synthetic biology


Abstract

The Joy of Cloning: Chimera, a Recipe for Integrating Computational Tools with Experimental Protocols
If BU can clone it, so can you! With a pinch of wet lab work and a dash of computational tools, we have developed a new recipe called Chimera that will help fellow synthetic biology cloners in the creation of their genetic devices! Chimera utilizes bio-design automation software tools with experimental protocols and builds upon a thoroughly characterized library of MoClo parts. This recipe, or workflow, integrates software tools to reduce human error and to structure the way device designs are chosen, assembled, and tested. To demonstrate that this workflow can be used by any level of cloner (beginner, intermediate, and advanced), we will highlight how we used Chimera to create:

  • individual genetic parts (namely tandem promoters, fusion proteins, and different backbones),

  • transcriptional units assembled from individual parts (with both new and previously made MoClo parts), and

  • a complex genetic device (our goal is a priority encoder).



    Click here to explore our project!
    •


    Our Sponsors

    Retrieved from "http://2014.igem.org/Team:BostonU"