Team:Uppsala/modeling

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<title>Uppsala iGEM 2013</title>
<title>Uppsala iGEM 2013</title>
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<div id="igem_logo"><a href="https://2013.igem.org/Main_Page"><img class="igem_logo" src="https://static.igem.org/mediawiki/2013/5/59/IGEMlogo.png"></a></div>
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<div id="igem_logo"><a href="https://2013.igem.org/Team:Uppsala"><img class="igem_logo" src="https://static.igem.org/mediawiki/2013/e/e0/Uppsala2013_IGEMlogo.png"></a></div>
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<li><a href="https://2013.igem.org/Team:Uppsala/project" id="list_type1"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/9/92/Project.png"></a>
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<li><a href="https://2013.igem.org/Team:Uppsala/project" id="list_type1"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/a/aa/Uppsala2013_Project.png"></a>
<ul>
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<li><a href="#">Result</a></li>
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<li><a href="#">Overview</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/chassi">Chassi</a>
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<li><a href="#">Chassi</a></li>
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<li><a href="#">Chromoprotein collection</a></li>
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                                                                <li><a href="https://2013.igem.org/Team:Uppsala/probiotics">Probiotics</a></li>
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<li><a href="#">Safety experiments</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/promoters">Promoters</a></li>
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<li><a href="#">Resveratrol</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/reporter-genes">Reporter genes</a></li>
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<li><a href="#">Caretnoids</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/toxin-antitoxin-system">Toxin-antitoxin system</a></li>
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<li><a href="#">Saffron</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/vectors">Vectors</a></li>
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<li><a href="#">Miraculin</a></li>
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                                                                <li><a href="https://2013.igem.org/Team:Uppsala/signal-peptide">Signal peptide</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/modeling" id="list_type1"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/3/3c/Modeling.png"></a>
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                                                <li><a href="https://2013.igem.org/Team:Uppsala/metabolic-engineering">Metabolic engineering</a>
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                                                                <li><a href="https://2013.igem.org/Team:Uppsala/p-coumaric-acid">p-Coumaric acid</a></li>
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                                                                <li><a href="https://2013.igem.org/Team:Uppsala/resveratrol">Resveratrol</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/lycopene">Lycopene</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/betacarotene">β-carotene</a></li>
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href="https://2013.igem.org/Team:Uppsala/saffron">Saffron</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/astaxanthin">Astaxanthin</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/zeaxanthin">Zeaxanthin</a></li>
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                                                <li><a
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href="https://2013.igem.org/Team:Uppsala/miraculin">Miraculin</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/chromoproteins">Chromoproteins</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/safety-experiment">Safety experiment</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/results">Results</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/modeling" id="list_type1"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/6/63/Uppsala2013_Modeling.png"></a>
<ul>
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<li><a href="#">Resveratrol pathway</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/P-Coumaric-acid-pathway">Kinetic model</a></li>
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<li><a href="#">Carotenoids pathway</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/modeling-tutorial">Modeling tutorial </a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/toxicity-model">Toxicity model</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/parts" id="list_type2"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/e/eb/Uppsala2013_parts.png"></a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/team" id="list_type2"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/3/32/Team.png"></a>
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<li><a href="https://2013.igem.org/Team:Uppsala/team" id="list_type2"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/a/a7/Uppsala2013_Team.png"></a>
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<li><a href="#">Resveratrol group</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/resveratrol-group">Resveratrol group</a></li>
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<li><a href="#">Carotenoid group</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/carotenoid-group">Carotenoid group</a></li>
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<li><a href="#">Chassi group</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/chassi-group">Chassi group</a></li>
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<li><a href="#">Instructors & supervisors</a></li>
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                                                <li><a href="https://2013.igem.org/Team:Uppsala/advisors">Advisors</a></li>
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</ul></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/hp" id="list_type3"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/f/f5/HP.png"></a>
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<li><a href="https://2013.igem.org/Team:Uppsala/human-practice" id="list_type3"><img class="nav-text"       src="https://static.igem.org/mediawiki/2013/b/b8/Uppsala2013_HP.png"></a>
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<li><a href="#">Yoghurt products</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/yoghurt">Yoghurt +</a></li>
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<li><a href="#">Synbioday</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/synbioday">SynBioDay</a></li>
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<li><a href="#">Bioethics</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/biosafety-and-ethics">Biosafety and ethics</a></li>
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<li><a href="#">Safety</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/public-opinion">Public opinion </a></li>
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<li><a href="#">Society / Public opinion</a></li>
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                                                <li><a href="https://2013.igem.org/Team:Uppsala/Outreach">High school & media </a></li>
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<li><a href="#">High School Outreach</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/bioart">BioArt</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/LactonutritiousWorld">A LactoWorld</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/killswitches">Killswitches</a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/realization">Patent</a></li>
</ul></li>
</ul></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/attribution" id="list_type4"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/8/8d/Attributions.png"></a></li>  
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<li><a href="https://2013.igem.org/Team:Uppsala/attribution" id="list_type4"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/5/5d/Uppsala2013_Attributions.png"></a></li>  
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<li><a href="https://2013.igem.org/Team:Uppsala/notebook" id="list_type3"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/9/95/Notebook.png"></a></li>
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<li><a href="https://2013.igem.org/Team:Uppsala/notebook" id="list_type3"><img class="nav-text" src="https://static.igem.org/mediawiki/2013/3/36/Uppsala2013_Notebook.png"></a>
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                                    <ul>
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                                        <li><a href="https://2013.igem.org/Team:Uppsala/safety-form">Safety form</a></li>
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                                        <li><a href="https://2013.igem.org/Team:Uppsala/protocols">Protocols</a></li>
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<h1 class="main-title">Modeling</h1>
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When we first set out to create this year's modeling contibution, we asked ourselves what we wanted from our project. None of us had much experience in the ways of modeling biological systems, so the first objective was to find inspiration for the project at hand. Naturally, the first place to look was the wikis of the teams that came before us. We wanted to see what other teams had accomplished, what they had brought to the table and perhaps what we thought could be improved in their modeling projects. After much searching, and more than a little contemplation, we arrived at the decision of making two different models, with two quite different goals.
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<h1>Goal number one: Applicability</h1>
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<div class="modeling_main_text_box"><a href="https://2013.igem.org/Team:Uppsala/P-Coumaric-acid-pathway" style="display:block;height:100%;width:100%">
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The goal of the first model was to create practical predictions about the systems we were about to create, and thus make better design decisions in order to achieve an optimal metabolite yield. This required a more sophisticated model that took into consideration all the complex parameters influencing a biological system. In the end, we managed to arrive to a model that did just that for the metabolic pathway producing p-Coumaric acid.
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The kinetic model for p-Coumaric acid production can be found <b>here</b> <a href="https://2013.igem.org/Team:Uppsala/P-Coumaric-acid-pathway" style="display:block;height:100%;width:100%">
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We have also made a toxicity evaluation of the content of our yoghurt which can be found in the menu above.
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<br><br>
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<h1>Goal number two: Accessability</h1>
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<div class="modeling_main_text_box"><a href="https://2013.igem.org/Team:Uppsala/modeling-tutorial" style="display:block;height:100%;width:100%">
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Our second goal with this year’s modeling project was to provide a more easy-to-access model aimed mainly to future iGEM teams. We found that while there are many excellent modeling contributions from earlier teams out there, the level of understanding required to take advantage of the information provided is quite high. Seeing as iGEM is an undergraduate competition, and not everyone participating have the requisite experience with systems like MATLAB, we figured that providing a comprehensive tutorial coupled with a simple model made within the bounds of a user-friendly interface would be a good contribution to this year’s modeling project. <br><br>
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<img class="figure_pic" src="https://static.igem.org/mediawiki/2013/2/27/Uppsala2013_ModelingDummies.png" style="border: 1px solid;">
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The tutorial for modeling can be found <b>here</b>
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Latest revision as of 18:27, 28 October 2013

Modeling

When we first set out to create this year's modeling contibution, we asked ourselves what we wanted from our project. None of us had much experience in the ways of modeling biological systems, so the first objective was to find inspiration for the project at hand. Naturally, the first place to look was the wikis of the teams that came before us. We wanted to see what other teams had accomplished, what they had brought to the table and perhaps what we thought could be improved in their modeling projects. After much searching, and more than a little contemplation, we arrived at the decision of making two different models, with two quite different goals.


Goal number one: Applicability



Goal number two: Accessability