Difference between revisions of "Team:William and Mary"

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{{William_and_Mary}}
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<html>
  
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<div class = "column full_size">
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<h2> Project Description </h2>
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<p><b>WM iGEM 2016 Presents: The Circuit Control Toolbox.</b></p>
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<p>Genetic circuits can be described according to their input-output relation by using a Transfer Function, which plots the concentration of output protein with respect to concentrations of input molecule. Such functions are well-modeled by Hill Functions, and as such have three parameters: the hill coefficient n, the half-max concentration K, and the saturation level V. These mathematical parameters correspond to the physical circuit properties of response steepness, input sensitivity, and maximal response level, respectively, in addition to the emergent properties which arise from their combinatorial modification.</p>
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<p>We present a toolbox of BioBrick parts that will allow for the modification of the Transfer Functions of arbitrary circuits via the incorporation of these parts into the final steps of the circuit. These parts include Decoy Binding Arrays, which buffer the sensitivity of the circuit to low levels of input concentration, promoters driven by synthetic enhancers to allow the circuit to reach up to four levels of discrete output levels, and a suite of ribosome binding sites to modulate the circuit's total output level. Our parts are all buffered by the inclusion of characterized ribozymes downstream of the promoter, in order to insulate the specific circuit component's transfer function from the choice of expressed protein, allowing for greater orthogonality and modularity in our toolbox components.</p>
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<p>In addition to creating, characterizing, and submitting these Toolbox parts to the Registry, we will also create a Circuit Toolbox Calculator which experimenters can use to navigate the high-dimensional space of possible Transfer Function modifications. Experimenters who have built a genetic circuit will input two transfer functions: their empirical observations of the circuit's response at different input molecule concentrations, and a desired transfer function for their modified circuit. The calculator then finds the optimal match to the target function by iterating through the possible modifications to the empirical transfer function through the parts in our Toolbox, returning to the user a list of Toolbox parts and small-molecule inducer concentrations that will replicate this best-match function <i>in vitro</i>. These calculations will be based on both theoretical and observational insights from mechanistic models and kinetic simulations of the interactions between our Toolbox components and arbitrary genetic circuits.</p>
  
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</div>
  
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<div class="column full_size" >
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<h2> Welcome to iGEM 2016! </h2>
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<p>Your team has been approved and you are ready to start the iGEM season! </p>
  
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</div>
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var $project_content;
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var test = true;       
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<div class="column half_size" >
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<h5>Before you start: </h5>
 +
<p> Please read the following pages:</p>
 +
<ul>
 +
<li>  <a href="https://2016.igem.org/Requirements">Requirements page </a> </li>
 +
<li> <a href="https://2016.igem.org/Wiki_How-To">Wiki Requirements page</a></li>
 +
<li> <a href="https://2016.igem.org/Resources/Template_Documentation"> Template Documentation </a></li>
 +
</ul>
 +
</div>
  
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var timerStart = Date.now();
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<div class="column half_size" >
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var delay;
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<div class="highlight">
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<h5> Styling your wiki </h5>
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<p>You may style this page as you like or you can simply leave the style as it is. You can easily keep the styling and edit the content of these default wiki pages with your project information and completely fulfill the requirement to document your project.</p>
 +
<p>While you may not win Best Wiki with this styling, your team is still eligible for all other awards. This default wiki meets the requirements, it improves navigability and ease of use for visitors, and you should not feel it is necessary to style beyond what has been provided.</p>
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</div>
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</div>
  
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<div class="column full_size" >
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var window_height;
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<h5> Wiki template information </h5>
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var window_width;
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<p>We have created these wiki template pages to help you get started and to help you think about how your team will be evaluated. You can find a list of all the pages tied to awards here at the <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions">Pages for awards</a> link. You must edit these pages to be evaluated for medals and awards, but ultimately the design, layout, style and all other elements of your team wiki is up to you!</p>
  
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    burger_menu = $('nav[role="navigation"]').hasClass('navbar-burger') ? true : false;
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<div class="column half_size" >
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<h5> Editing your wiki </h5>
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    if (!Modernizr.touch){
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<p>On this page you can document your project, introduce your team members, document your progress and share your iGEM experience with the rest of the world! </p>
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        $('body').addClass('no-touch');
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<p> <a href="https://2016.igem.org/wiki/index.php?title=Team:Example&action=edit"> </a>Use WikiTools - Edit in the black menu bar to edit this page</p>
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<div class="column half_size" >
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<h5>Tips</h5>
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<p>This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started: </p>
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<ul>
 +
<li>State your accomplishments! Tell people what you have achieved from the start. </li>
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<li>Be clear about what you are doing and how you plan to do this.</li>
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<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
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<li>Make sure information is easy to find; nothing should be more than 3 clicks away.  </li>
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<li>Avoid using very small fonts and low contrast colors; information should be easy to read.  </li>
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<li>Start documenting your project as early as possible; don’t leave anything to the last minute before the Wiki Freeze. For a complete list of deadlines visit the <a href="https://2016.igem.org/Calendar">iGEM 2016 calendar</a> </li>
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<li>Have lots of fun! </li>
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</ul>
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</div>
  
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<h5>Inspiration</h5>
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    if($(window).width() < 992){
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<p> You can also view other team wikis for inspiration! Here are some examples:</p>
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        rubik.initRightMenu(); 
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<ul>
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        rubik.checkResponsiveImage();
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<li> <a href="https://2014.igem.org/Team:SDU-Denmark/"> 2014 SDU Denmark </a> </li>
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    }
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<li> <a href="https://2014.igem.org/Team:Aalto-Helsinki">2014 Aalto-Helsinki</a> </li>
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<li> <a href="https://2014.igem.org/Team:LMU-Munich">2014 LMU-Munich</a> </li>
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        $('nav[role="navigation"]').removeClass('navbar-burger');
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<li> <a href="https://2014.igem.org/Team:Michigan"> 2014 Michigan</a></li>
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<li> <a href="https://2014.igem.org/Team:ITESM-Guadalajara">2014 ITESM-Guadalajara </a></li>
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<li> <a href="https://2014.igem.org/Team:SCU-China"> 2014 SCU-China </a></li>
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    }
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</ul>
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});
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</div>
  
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$(window).on('scroll',function(){
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<div class="column half_size" >
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  rubik.checkScrollForTransparentNavbar();   
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<h5> Uploading pictures and files </h5>
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<p> You can upload your pictures and files to the iGEM 2016 server. Remember to keep all your pictures and files within your team's namespace or at least include your team's name in the file name. <br />
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  if(window_width > 992){
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When you upload, set the "Destination Filename" to <br><code>T--YourOfficialTeamName--NameOfFile.jpg</code>. (If you don't do this, someone else might upload a different file with the same "Destination Filename", and your file would be erased!)</p>
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$('.section-we-made-2 .scroller').mousemove(
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<div class="button_click" onClick=" parent.location= 'https://2016.igem.org/Special:Upload '"> 
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UPLOAD FILES
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        $('.projects').css('overflow','hidden');
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);
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    initRightMenu: function(){ 
 
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        if(!navbar_initialized){
 
−
            $nav = $('nav[role="navigation"]');
 
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            $nav.addClass('navbar-burger');
 
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            $navbar = $nav.find('.navbar-collapse').first().clone(true);
 
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            ul_content = '';
 
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            $navbar.children('ul').each(function(){
 
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                ul_content = ul_content + content_buff; 
 
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            ul_content = '<ul class="nav navbar-nav">' + ul_content + '</ul>';
 
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            $navbar.html(ul_content);
 
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            background_image = $navbar.data('nav-image');
 
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                $navbar.css('background',"url('" + background_image + "')")
 
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            $navbar.find('a').removeClass('btn btn-round btn-default');
 
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                if(scroll_trigger == true && scroll_target !== undefined){
 
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            $('.section-header > div > img, .section-header video').each(function(){
 
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//JOHN MITCHELL modify distance from top at which navbar becomes opaque, lowered for new page
 
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−
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    checkScrollForContentTransitions: debounce(function() {
 
−
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−
            var $content = $(this);
 
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                      return;
 
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                    $content.css('opacity',opacityVal);   
 
−
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−
    }, 6),
 
−
   
 
−
    showModal: function(button){
 
−
        var id = $(button).data('target');
 
−
        var $project = $(button).closest('.project');
 
−
       
 
−
        var scrollTop = $(window).scrollTop();
 
−
        var distanceTop = $project.offset().top;
 
  
−
        var projectTop = distanceTop - scrollTop;
+
</html>
−
        var projectLeft = $project.offset().left;
+
−
        var projectHeight = $project.innerHeight();
+
−
        var projectWidth = $project.innerWidth();
+
−
 
+
−
        modal = $('#' + id);
+
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+
−
        $(modal).css({
+
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        'top'  :    projectTop,
+
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        'left' :    projectLeft,
+
−
        'width' :  projectWidth,
+
−
        'height' :  projectHeight,
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Revision as of 01:24, 5 October 2016

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Project Description

WM iGEM 2016 Presents: The Circuit Control Toolbox.

Genetic circuits can be described according to their input-output relation by using a Transfer Function, which plots the concentration of output protein with respect to concentrations of input molecule. Such functions are well-modeled by Hill Functions, and as such have three parameters: the hill coefficient n, the half-max concentration K, and the saturation level V. These mathematical parameters correspond to the physical circuit properties of response steepness, input sensitivity, and maximal response level, respectively, in addition to the emergent properties which arise from their combinatorial modification.

We present a toolbox of BioBrick parts that will allow for the modification of the Transfer Functions of arbitrary circuits via the incorporation of these parts into the final steps of the circuit. These parts include Decoy Binding Arrays, which buffer the sensitivity of the circuit to low levels of input concentration, promoters driven by synthetic enhancers to allow the circuit to reach up to four levels of discrete output levels, and a suite of ribosome binding sites to modulate the circuit's total output level. Our parts are all buffered by the inclusion of characterized ribozymes downstream of the promoter, in order to insulate the specific circuit component's transfer function from the choice of expressed protein, allowing for greater orthogonality and modularity in our toolbox components.

In addition to creating, characterizing, and submitting these Toolbox parts to the Registry, we will also create a Circuit Toolbox Calculator which experimenters can use to navigate the high-dimensional space of possible Transfer Function modifications. Experimenters who have built a genetic circuit will input two transfer functions: their empirical observations of the circuit's response at different input molecule concentrations, and a desired transfer function for their modified circuit. The calculator then finds the optimal match to the target function by iterating through the possible modifications to the empirical transfer function through the parts in our Toolbox, returning to the user a list of Toolbox parts and small-molecule inducer concentrations that will replicate this best-match function in vitro. These calculations will be based on both theoretical and observational insights from mechanistic models and kinetic simulations of the interactions between our Toolbox components and arbitrary genetic circuits.

Welcome to iGEM 2016!

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