Difference between revisions of "Team:UMaryland/Model"

(Prototype team page)
 
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{{UMaryland}}
 
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<html>
 
  
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</div>
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</div>
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<html lang="en">
  
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<div class="column full_size judges-will-not-evaluate">
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<head>
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<h3>★  ALERT! </h3>
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    <script>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2016.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>. </p>
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        $('body').css('display', 'none');
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    </script>
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    <script src="https://static.igem.org/mediawiki/2016/9/95/T--UMaryland--html5shiv.txt"></script>
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    <script src="https://static.igem.org/mediawiki/2016/c/ce/T--UMaryland--parallax.txt"></script>
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    <script src="https://static.igem.org/mediawiki/2016/d/d3/T--UMaryland--slick.txt" type="text/javascript"></script>
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    <title>Modeling</title>
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</head>
  
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<body>
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    <style>
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        @font-face {
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            font-family: 'Exo';
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            font-style: normal;
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            font-weight: 400;
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            src: url(https://static.igem.org/mediawiki/2016/0/02/T--UMaryland--Exo.woff) format('woff2');
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        }
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        @font-face {
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            font-family: 'Lora';
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            font-style: normal;
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            font-weight: 400;
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            src: url(https://static.igem.org/mediawiki/2016/6/61/T--UMaryland--Lora.woff) format('woff2');
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        }
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        @font-face {
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            font-family: 'Raleway';
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            font-style: normal;
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            font-weight: 200;
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            src: url(https://static.igem.org/mediawiki/2016/b/b7/T--UMaryland--RalewayLight.woff) format('woff2');
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        }
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        @font-face {
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            font-family: 'Raleway';
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            font-style: normal;
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            font-weight: 400;
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<style>
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/* Slider */ .slick-slider { position: relative; display: block; box-sizing: border-box; -webkit-user-select: none; -moz-user-select: none; -ms-user-select: none; user-select: none; -webkit-touch-callout: none; -khtml-user-select: none; -ms-touch-action: pan-y; touch-action: pan-y; -webkit-tap-highlight-color: transparent; } .slick-list { position: relative; display: block; overflow: hidden; margin: 0; padding: 0; } .slick-list:focus { outline: none; } .slick-list.dragging { cursor: pointer; cursor: hand; } .slick-slider .slick-track, .slick-slider .slick-list { -webkit-transform: translate3d(0, 0, 0); -moz-transform: translate3d(0, 0, 0); -ms-transform: translate3d(0, 0, 0); -o-transform: translate3d(0, 0, 0); transform: translate3d(0, 0, 0); } .slick-track { position: relative; top: 0; left: 0; display: block; } .slick-track:before, .slick-track:after { display: table; content: ''; } .slick-track:after { clear: both; } .slick-loading .slick-track { visibility: hidden; } .slick-slide { display: none; float: left; height: 100%; min-height: 1px; } [dir='rtl'] .slick-slide { float: right; } .slick-slide img { display: block; } .slick-slide.slick-loading img { display: none; } .slick-slide.dragging img { pointer-events: none; } .slick-initialized .slick-slide { display: block; } .slick-loading .slick-slide { visibility: hidden; } .slick-vertical .slick-slide { display: block; height: auto; border: 1px solid transparent; } .slick-arrow.slick-hidden { display: none; } .slick-arrow { background-color: #B0B0B0;}
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<style>
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@charset 'UTF-8'; /* Slider */ .slick-loading .slick-list { background: #fff url('https://static.igem.org/mediawiki/2016/8/85/T--UMaryland--ajax-loader.gif') center center no-repeat; } /* Icons */ @font-face { font-family: 'slick'; font-weight: normal; font-style: normal; src: url('./fonts/slick.eot'); src: url('./fonts/slick.eot?#iefix') format('embedded-opentype'), url('https://static.igem.org/mediawiki/2016/a/a9/T--UMaryland--slick.woff') format('woff'), url('https://static.igem.org/mediawiki/2016/b/b8/T--UMaryland--slick.ttf') format('truetype'), url('./fonts/slick.svg#slick') format('svg'); } /* Arrows */ .slick-prev, .slick-next { font-size: 0; line-height: 0; position: absolute; top: 50%; display: block; width: 20px; height: 20px; padding: 0; -webkit-transform: translate(0, -50%); -ms-transform: translate(0, -50%); transform: translate(0, -50%); cursor: pointer; color: transparent; border: none; outline: none; background: transparent; } .slick-prev:hover, .slick-prev:focus, .slick-next:hover, .slick-next:focus { color: transparent; outline: none; background: transparent; } .slick-prev:hover:before, .slick-prev:focus:before, .slick-next:hover:before, .slick-next:focus:before { opacity: 1; } .slick-prev.slick-disabled:before, .slick-next.slick-disabled:before { opacity: .25; } .slick-prev:before, .slick-next:before { font-family: 'slick'; font-size: 25px; line-height: 1; opacity: .75; color: #808080; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } .slick-prev { left: -25px; } [dir='rtl'] .slick-prev { right: -25px; left: auto; } .slick-prev:before { content: '←'; } [dir='rtl'] .slick-prev:before { content: '→'; } .slick-next { right: -25px; } [dir='rtl'] .slick-next { right: auto; left: -25px; } .slick-next:before { content: '→'; } [dir='rtl'] .slick-next:before { content: '←'; } /* Dots */ .slick-dotted.slick-slider { margin-bottom: 30px; } .slick-dots { position: absolute; bottom: -25px; display: block; width: 100%; padding: 0; margin: 0; list-style: none; text-align: center; } .slick-dots li { position: relative; display: inline-block; width: 20px; height: 20px; margin: 0 5px; padding: 0; cursor: pointer; } .slick-dots li button { font-size: 0; line-height: 0; display: block; width: 20px; height: 20px; padding: 5px; cursor: pointer; color: transparent; border: 0; outline: none; background: transparent; } .slick-dots li button:hover, .slick-dots li button:focus { outline: none; } .slick-dots li button:hover:before, .slick-dots li button:focus:before { opacity: 1; } .slick-dots li button:before { font-family: 'slick'; font-size: 6px; line-height: 20px; position: absolute; top: 0; left: 0; width: 20px; height: 20px; content: '•'; text-align: center; opacity: .25; color: black; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } .slick-dots li.slick-active button:before { opacity: .75; color: black; }
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</style>
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<style>
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@charset "UTF-8";
  
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<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p>
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/*!
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</div>
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* animate.css -http://daneden.me/animate
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* Version - 3.5.1
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* Licensed under the MIT license - http://opensource.org/licenses/MIT
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*
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* Copyright (c) 2016 Daniel Eden
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*/
  
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slideOutUp{0%{-webkit-transform:translateZ(0);transform:translateZ(0)}to{visibility:hidden;-webkit-transform:translate3d(0,-100%,0);transform:translate3d(0,-100%,0)}}.slideOutUp{-webkit-animation-name:slideOutUp;animation-name:slideOutUp}
 +
</style>
 +
 +
<style>
 +
/* Permanent bottom bar */
 +
 +
#bot-nav {
 +
    background-color: #f9f9f9;   
 +
    border-top: 1px solid #f5f5f5;
 +
    position: absolute;
 +
    width: 100%;
 +
    height: 100px;
 +
    display: block;
 +
    color: black;
 +
    font-size: 12pt;
 +
    font-family: 'Lora', serif;
 +
    z-index: -1;
 +
}
  
 +
#social-media {
 +
width: 100%;
 +
margin:0 0 0 0;
 +
}
 +
.pull-right a {
 +
padding-right: 0px !important;
 +
}
  
 +
.copyright {
 +
text-align: center;
 +
width: 272px;
 +
height: 30px;
 +
margin-top: -20px;
 +
margin-left: auto;
 +
margin-right: auto;
 +
}
  
 +
.pull-left {
 +
margin-top: -3px;
 +
width: 83px;
 +
margin-left: 30px;
 +
margin-right: auto;
 +
display: inline;
 +
height: 34px;
 +
}
  
 +
.pull-left p {
 +
margin: 0 0 0 0;
 +
padding: 0 0 0 0 !important;
 +
line-height: 0px !important;
 +
}
  
 +
.pull-right {
 +
width: 83px;
 +
margin-right: 30px;
 +
margin-left: auto;
 +
}
  
−
<div class="column full_size">
+
#copyright {
−
<h2> Modeling</h2>
+
    text-align: center;
−
<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
+
left:auto;
 +
right: auto;
 +
width: 100%;
 +
padding: 0 0 0 0;
 +
margin-top: 0px;
 +
float:left;
 +
}
  
 +
#container {
 +
    max-width: 1200px;
 +
    margin-left: auto;
 +
    margin-right: auto;
 +
margin-top: 40px;
 +
}
  
−
<h5> Inspiration </h5>
+
#container img {
−
<p>
+
    height: 20px;
−
Here are a few examples from previous teams:
+
    width: 20px;
−
</p>
+
    -webkit-filter: grayscale(100%);
−
<ul>
+
    filter: grayscale(100%);
−
<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
+
}
−
<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
+
−
</ul>
+
  
 +
#bot-nav img:hover {
 +
    -webkit-filter: grayscale(0%);
 +
    filter: grayscale(0%);
 +
}
  
−
</div>
+
#container li {
 +
    display: inline;
 +
list-style:none;
 +
padding-right: 25px;
 +
}
 +
 
 +
.pull-left {
 +
float:left;
 +
}
 +
 
 +
#bot-nav a {
 +
    text-decoration: none;
 +
    color: black;
 +
}
 +
 
 +
#contact:hover {
 +
    text-shadow: .1px .1px black;
 +
}
 +
</style>
 +
    <style>
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font-weight: bold;
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background-color: transparent;
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<nav>
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<img src="https://static.igem.org/mediawiki/2016/2/26/T--UMaryland--newlogo.jpeg" id="img-logo" width="128px">
 +
<ul>
 +
<a style="opacity: 0">Fix</a>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/projects">Projects</a></li>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/parts">Parts</a></li>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/modeling">Modeling</a></li>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/outreach">Outreach</a></li>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/notebook">Notebook</a></li>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/about">About Us</a></li>
 +
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 +
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 +
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<!-- Nav bar when more button is clicked -->
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 +
<img src="https://static.igem.org/mediawiki/2016/2/26/T--UMaryland--newlogo.jpeg" id="img-logoResized">
 +
<ul>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/projects">Projects</a></li>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/parts">Parts</a></li>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/modeling">Modeling</a></li>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/outreach">Outreach</a></li>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/notebook">Notebook</a></li>
 +
<li><a href="https://2016.igem.org/Team:UMaryland/about">About Us</a></li>
 +
</ul>
 +
</div>
 +
<div data-parallax="scroll" data-image-src="https://static.igem.org/mediawiki/2016/a/a8/T--UMaryland--smmo.jpg" id="div-pic">
 +
<div class="titleText">
 +
<!-- where background image below titles show -->
 +
<h11>Modeling</h11>
 +
<h21>Predicitng Data and Optimizing Results</h21>
 +
<h31>Applying engineering principals to biological systems</h31>
 +
</div>
 +
        </div>
 +
<div id="div-text"> <!-- Start of main text of page -->
 +
<!-- Heading text -->
 +
 +
 +
<div class="longText">
 +
<p>Modeling is crucial to designing biological systems such as ours, where we want both predictability and optimization of our organism. We used the SimBiology package in MatLab in order to model our multiple metabolic pathways using data gathered experimentally and from literature. We then optimized the parameters to determine what the optimal growth conditions of our organisms will be in order to most efficiently biosequester methane.</p>
 +
</div>
 +
<div class="longText">
 +
<h4>Pathways</h4>
 +
<p>Three different constructs were synthesized by UMaryland iGEM in hopes of being co-cultured. They were:</p>
 +
<ul>
 +
<li>sMMO Construct: oxidizing methane into methanol using oxygen</li>
 +
<li>Formate Construct: further oxidizing methanol into carbon dioxide using NADH</li>
 +
<li>Fructose Construct: further oxidizing methanol into cellular metabolites</li>
 +
</ul>
 +
</div>
 +
<div class="longText" id="div-protocol">
 +
<h4>Protocol</h4>
 +
</div>
 +
<div class="longText">
 +
<h4>Results</h4>
 +
<div id="div-results">
 +
</div>
 +
<div id="div-figures">
 +
<div>
 +
<img class="figure" src="https://static.igem.org/mediawiki/2016/a/ae/T--UMaryland--absorbance.JPG">
 +
<small class="caption">Figure 1. Cell growth versus absorbance.</small>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
    <div id="bot-nav">
 +
        <div id="container">
 +
            <div class="pull-left">
 +
                <a href="mailto:umarylandigem@gmail.com"><p id="contact"> Contact Us </p></a>
 +
            </div>
 +
            <div class="pull-right">
 +
                <ul id="social-media">
 +
                    <li> <a href="https://www.facebook.com/UMarylandiGEM/"> <img src="https://static.igem.org/mediawiki/2016/9/9f/T--UMaryland--fbLogo.jpeg"/> </a> </li>
 +
                    <li> <a href="https://www.instagram.com/umarylandigem/"> <img src="https://static.igem.org/mediawiki/2016/c/ca/T--UMaryland--instalogo.jpg"/> </a> </li>
 +
                </ul>
 +
            </div>
 +
        </div>
 +
<div class="copyright">
 +
            <p id="copyright">© University of Maryland iGEM 2016</p>
 +
</div>
 +
    </div>
 +
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</div> </div> Modeling

Modeling Predicitng Data and Optimizing Results Applying engineering principals to biological systems

Modeling is crucial to designing biological systems such as ours, where we want both predictability and optimization of our organism. We used the SimBiology package in MatLab in order to model our multiple metabolic pathways using data gathered experimentally and from literature. We then optimized the parameters to determine what the optimal growth conditions of our organisms will be in order to most efficiently biosequester methane.

Pathways

Three different constructs were synthesized by UMaryland iGEM in hopes of being co-cultured. They were:

  • sMMO Construct: oxidizing methane into methanol using oxygen
  • Formate Construct: further oxidizing methanol into carbon dioxide using NADH
  • Fructose Construct: further oxidizing methanol into cellular metabolites

Protocol

Results

Figure 1. Cell growth versus absorbance.