Difference between revisions of "Team:KU Leuven/Modeling/Internal/Ultra/Test"

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<html>
 
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<title> Ultra Test </title>
 
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<meta charset="utf-8">
 
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</style>
 
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<head>
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<link rel="icon" href="https://static.igem.org/mediawiki/2015/9/9c/Ku_Leuven_Favicon.gif" />
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<link rel="shortcut icon" href="https://static.igem.org/mediawiki/2015/9/9c/Ku_Leuven_Favicon.gif" /
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<body>
 
<body>
  
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<div class="summaryheader">
 
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  <div class="summaryimg">
 
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  <img src="https://static.igem.org/mediawiki/2015/e/eb/KU_Leuven_fossilBackground.png" width="100%">
 
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  <div class="head">
 
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    <h2> Internal Model </h2>
 
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  </div>
 
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<!------------------------------------------------------Begin Content------------------------------------------------------->
 
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<div class="summarytext1">
 
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<div class="part">
 
  
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<div class="onoffswitch">
 
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    <input type="checkbox" name="onoffswitch" class="onoffswitch-checkbox" id="EasySwitch" onchange="EasySwitch()" onmouseover="WhatSwitch()" style="cursor:Pointer;" title="Find out more about James Bond and his line of work">
 
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    <label class="onoffswitch-label" for="EasySwitch">
 
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        <span class="onoffswitch-inner" title="Press me please"></span>
 
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    </label>
 
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</div>
 
  
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<div class="scientific">
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<div id="headimg">
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<h3> 0.5 Test </h3>
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<div id="topimg">
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<p> This is a very difficult text.
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</p>
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</div>
 
</div>
  
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<div class="easy">
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<div id="hiddenimg">
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<h3> 0.5 Test </h3>
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  <img src="https://static.igem.org/mediawiki/2015/b/bb/KU_Leuven_Zebra2.PNG" width="100%">
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<p> This is a very easy text. </p>
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</div>
 
</div>
  
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<div id="VincentEaster" style="display: none">
 
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<img id="VincentRipped" src="https://scontent-ams3-1.xx.fbcdn.net/hphotos-xpa1/t31.0-8/s960x960/11059591_847950888629027_4500642809718564299_o.jpg" alt="Cell A" height="100%" width="100%" onmouseover="Vinnie()">
 
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</div>
 
  
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<div id="Left1" class="easyleft">
 
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<p>En alle beelden op tv<br/>
 
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Van bloed en oorlog om ons heen<br/>
 
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Werken daar ook niet echt aan mee</p>
 
 
</div>
 
</div>
  
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<div>
 
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<h2> 1. Introduction </h2>
 
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<p style="cursor:Pointer;" title="Find out more about James Bond and his line of work">My name is James Bond</p>
 
  
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<p id="Introduction">
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<div id="summarywrapper">
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<div id="logowrapper">
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    In designing new circuits and implementing them, it is important to model the effect of it on the bacteria: how sensitive is the system, how much will it produce and will it affect the growth? These questions can be answerred in the internal model. We will use two approaches. Flux Balance Analysis (FBA) will study the steady-state values for production and growth rate, while  Simbiology will study the sensitivity and dynamic processes in the cell.
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<div id="logoiGEMKUL">
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</p>
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  <img src="https://static.igem.org/mediawiki/2015/2/23/Team_KU_Leuven_banner.jpg"  alt="Logo" width="100%" >
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<br>
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<br>
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</div>
 
</div>
  
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<div id="Simbiology" class="scientific">
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<div id="center">
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<h2> 2. Simbiology </h2>   
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<div id="pagetitle">
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<p>
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<h2>Our project</h2>
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In the next section we will describe our Simbiology model. Simbiology allows us to calculate systems of ODE's and to visualize them in a nice diagram. It also has options to make scans for different parameters which allows us to study the effect of the specified parameter. We will focus on the production of leucine, Ag43 and AHL in cell A and the changing behavior of cell B due to changing AHL concentration. In this perspective, we will make two models in Simbiology: one for cell A and cell B.
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−
</p>
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</div>
 
</div>
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<br>
 
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<br>
 
  
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<div class="easy">
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<div id="scrolldown" class="center">
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<h2> 2.1 Cell A </h2>
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<img src="https://static.igem.org/mediawiki/2015/1/1d/KU_Leuven_Arrows_wiki.png" alt="Scroll down" width="100%">
−
   
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</div>
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<p style='word-wrap:break-word'>
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−
The designed circuit in Cell A is under control of a temperature sensitive cI repressor. Upon raising the temperature, the circuit is activated and production of LuxR and LuxI initiates. LuxI will consectively produce AHL, which binds with LuxR to activate the production of Leucine and Ag43. We can extract the following ODE's from this circuit:
+
−
<br>
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−
${\alpha}$:transcription term, ${\beta}$:translation term, ${d}$:degradation term, ${D}$:diffusion term
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−
${K_d}$:dissociation constant, ${n}$:hill coefficient, ${L}$:leak term
+
  
−
    $$\frac{{\large d} m_{cI}}{d t} = \alpha_1 {\cdot} cI_{gene} - d_{mCI} {\cdot} m_{cI}$$
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</div>
−
    $$\frac{{\large d}{cI}}{d t} = \beta_{cI} {\cdot} {cI} -2 {\cdot} {k_{cI,dim}} {\cdot} {cI}^2 + 2 {\cdot}{k_{-cI,dim}}{\cdot} {[cI]_2} - d_{cI} {\cdot} {cI}$$
+
−
    $$\frac{{\large d}{[cI]_2}}{d t}= k_{cI,dim} {\cdot} {cI}^2 - {k_{-cI,dim}}{\cdot} {[cI]_2} $$
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−
    $$\frac{{\large d} m_{LuxI}}{d t} = (L_{lambda} + {\frac{\alpha_{lambda}}{1 + ({\frac{[cI]_2}{K_{d1}}})^{n_{cI}}}}) {\cdot} LuxI_{gene} - d_{mLuxI} {\cdot} m_{LuxI} $$
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−
    $$\frac{{\large d} m_{LuxR}}{d t} = (L_{lambda} + {\frac{\alpha_{lambda}}{1 + ({\frac{[cI]_2}{K_{d1}}})^{n_{cI}}}}) {\cdot} LuxR_{gene} - d_{mLuxR} {\cdot} m_{LuxR} $$
+
−
    $$\frac{{\large d} LuxI}{d t} = \beta_{LuxI} {\cdot} {m_{LuxI}} - d_{LuxI} {\cdot}{LuxI} $$
+
−
    $$\frac{{\large d} LuxR}{d t} = \beta_{LuxR} {\cdot} {m_{LuxR}} -k_{lux,as} {\cdot}{LuxR}{\cdot}{AHL_{in}} + k_{lux,dis}{\cdot}{[LuxR/AHL]} - d_{LuxR} {\cdot}{LuxR} $$
+
−
    $$\frac{{\large d} AHL_{in}}{d t} = {k_{luxI}} {\cdot} {luxI} - k_{lux,as} {\cdot}{luxR}{\cdot}{AHL_{in}} + k_{lux,dis}{\cdot}{[luxR/AHL]}+ ( {D_{IN,AHL}} {\cdot} {AHL_{out}} - {D_{OUT,AHL}} {\cdot} {AHL_{in}} ) - d_{AHL,in} {\cdot} {AHL_{in}}$$
+
−
    $$\frac{{\large d} AHL_{out}}{d t} = ( {D_{OUT,AHL}} {\cdot} {AHL_{in}} - {D_{IN,AHL}}{\cdot}{AHL_{out}} ) -d_{AHL,out}{\cdot}{AHL_{out}}$$
+
−
    $$\frac{{\large d} [luxR/AHL]}{d t} = k_{lux,as} {\cdot}{luxR}{\cdot}{AHL_{in}} - k_{lux,dis}{\cdot}{[luxR/AHL]} - 2 {\cdot} k_{lux,dim} {\cdot}{[luxR/AHL]^2} + 2 {\cdot}{k_{-lux,dim}}{\cdot}{[luxR/AHL]_{2}}$$
+
−
    $$\frac{{\large d} [luxR/AHL]_{2}}{d t} = k_{lux,dim} {\cdot}{[luxR/AHL]^2} - k_{- lux,dim} {[luxR/AHL]} $$
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−
    $$\frac{{\large d} m_{ilvE}}{d t} = (L_{lux} + \frac{\alpha_{lux}}{1+(\frac{K_{d2}}{[luxR/AHL]_{2}})^{n_{lux}}} ) {\cdot} ilvE_{gene} - d_{milvE} {\cdot} {m_{ilvE}} $$
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−
    $$\frac{{\large d} m_{Ag43}}{d t} = (L_{lux} + \frac{\alpha_{lux}}{1+(\frac{K_{d2}}{luxR/AHL]_{2}})^{n_{lux}}} ) {\cdot} Ag43_{gene} - d_{mAg43} {\cdot} {m_{Ag43}} $$
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    $$\frac{{\large d} Transaminase B}{d t} = \beta_{TB} {\cdot} {m_{ilvE}} - d_{TB} {\cdot} {Transaminase B} $$
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    $$\frac{{\large d} Leucine_{out}}{d t} = (D_{OUT,Leu} {\cdot}{leucine_{in}} - D_{IN,Leu} {\cdot}{leucine_{out}}) - d_{Leu,out} {\cdot} {Leucine_{out}} $$
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−
    $$\frac{{\large d} Ag43}{d t} = \beta_{Ag43} {\cdot} {m_{Ag43}} - d_{Ag43} {\cdot} {Ag43} $$
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 +
<div id="summarylogos">
  
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We visualize these ODE's in Simbiology which results in the following diagram:
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<div id="summarylogotwitter">
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</p>
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<a href="https://twitter.com/kuleuven_igem" height="100%"><img src="https://static.igem.org/mediawiki/2015/b/b8/KU_Leuven_Twitter-logo.png" alt="Twitter" width="100%"></a> 
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</div>
  
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<img id="simcellA" src="https://static.igem.org/mediawiki/2015/f/f7/KUL_IM_SIM_CB_TV1.png" alt="Cell A" height="100%" width="100%" onclick="bigImg(this)" onclick="normalImg(this)">
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<div id="summarylogofacebook">
 +
<a href="https://www.facebook.com/KULeuveniGEM?fref=ts" alt="Facebook" height="50px"><img src="https://static.igem.org/mediawiki/2015/d/df/KU_Leuven_Fblogo.png" alt="mail" width="100%"></a> 
 
</div>
 
</div>
  
 +
<div id="summarylogomail">
 +
<a href="mailto:igem@chem.kuleuven.be"><img src="https://static.igem.org/mediawiki/2015/1/11/KU_Leuven_mail.png" alt="mail" width="100%"></a> 
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</div>
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</div>
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</div>
 +
<div class="summary">
 +
<p>Test test ultra test
 +
Patterns are fascinating, from the veins of a leaf to the stripes of a zebra. Patterns are found everywhere in nature, but how they are formed is not entirely clear. We, the KU Leuven iGEM 2015 team, decided to work on the fundamental mechanisms behind pattern formation. The way cells of multicellular organisms interact to generate a specific pattern has triggered our curiosity. Our mission is to create astonishing biological patterns with engineered bacteria on a petri dish to unravel the secrets of nature. We will design a ‘proof of principle’ which can form the basis for fundamental research.<br>
 
<br>
 
<br>
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Project/About"><img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" alt="Read more" height="2.5%" width="10%"></a>
 +
</p>
 
<br>
 
<br>
 
<br>
 
<br>
 +
<div class="center">
 +
        <div class="quote" style="width:85%;">
 +
<p><h2>A last message of the team</h2></p>
 +
<p> We are back from the Jamboree!! <br> <br>
 +
We were very happy to present our results to the jury and we got a positive feedback: <br> <br>
 +
First we won a gold medal!! <br> <br>
 +
And we were even nominated for 4 prices in the overgrad section: Best Poster, Best Education and Public Engagement, Best Modeling and Best New Application Project in which we were the runner-up! <br> <br>
 +
We were very happy with these results and want to thank everybody involved who helped us to achieve this! Thank you very much!! </p>
 +
</div>
 +
</div>
 
<br>
 
<br>
 +
<div id="VincentEaster" style="display: none">
 +
<img id="Cat" src="http://www.troll.me/images/science-cat/happy-birthday-from-science-cat-thumb.jpg" height="100%" width="100%">
 +
<img id="VincentRipped" src="https://static.igem.org/mediawiki/2013/c/c6/Base_gift_345_259.JPG" alt="Cell A" height="100%" width="100%" onmouseover="Vinnie()">
 +
</div>
 +
</div>
  
−
<h2> 2.1 Cell B </h2>
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</div>
  
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<p>
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<div class="subsections">
−
We can repeat this assignment for Cell B:
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<div class="subsectionwrapper">
−
$$\frac{{\large d} m_{cI}}{d t} = \alpha_1 {\cdot} cI_{gene} - d_1 {\cdot} m_{cI}$$
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<div class="subimgrow">
−
    $$\frac{{\large d}{cI}}{d t} = \beta_1 {\cdot} {cI} -2 {\cdot} {k_{cI,dim}} {\cdot} {cI}^2 + 2 {\cdot}{k_{-cI,dim}}{\cdot} {[cI]_2} - d_{cI} {\cdot} {cI}$$
+
<div class="subimg">
−
    $$\frac{{\large d}{[cI]_2}}{d t}= k_{cI,dim} {\cdot} {cI}^2 - {k_{-cI,dim}}{\cdot} {[cI]_2} $$
+
<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
−
    $$\frac{{\large d} m_{luxR}}{d t} = (L_{lambda} + {\frac{\alpha_{lambda}}{1 + ({\frac{cI}{K_{d1}}})^{n_{cI}}}}) {\cdot} luxR_{gene} - d_{mluxR} {\cdot} m_{luxR} $$
+
<img src="https://static.igem.org/mediawiki/2015/1/1a/KUL_Wiki_Button_-_Project.png" width="100%">
−
    $$\frac{{\large d} luxR}{d t} = \beta_{luxR} {\cdot} {m_{luxR}} - d_{luxR} {\cdot}{luxR} $$
+
</a>
−
    $$\frac{{\large d} AHL_{in}}{d t} = ( {D_{IN,AHL}} {\cdot} {AHL_{out}} - {D_{OUT,AHL}} {\cdot} {AHL_{in}} ) - k_{lux,as}{\cdot}{luxR}{\cdot}{AHL_{in}} + k_{lux,dis}{\cdot}{[luxR/AHL]} - d_{AHL,in} {\cdot} {AHL_{in}} $$
+
</div>
−
    $$\frac{{\large d} AHL_{out}}{d t} = ( {D_{OUT,AHL}} {\cdot} {AHL_{in}} - {D_{IN,AHL}}{\cdot}{AHL_{out}} ) -d_{AHL,out}{\cdot}{AHL_{out}} $$
+
−
    $$\frac{{\large d} [luxR/AHL]}{d t} = k_{lux,as} {\cdot}{luxR}{\cdot}{AHL_{in}} - k_{lux,dis}{\cdot}{[luxR/AHL]} - 2 {\cdot} k_{lux,dim} {\cdot}{[luxR/AHL]^2} + 2 {\cdot}{[luxR/AHL]_{2}} $$
+
−
    $$\frac{{\large d} [luxR/AHL]_{2}}{d t} = k_{lux,dim} {\cdot}{[luxR/AHL]^2} - k_{- lux,dim} {[luxR/AHL]} $$
+
−
    $$\frac{{\large d} m_{CheZ}}{d t} = (L_{lux} + \frac{\alpha_{lux}}{1+(\frac{K_{d2}}{[luxR/AHL]_{2}})^{n_{lux}}} ) {\cdot} CheZ_{gene} - d_{mCheZ} {\cdot} {m_{CheZ}} $$
+
−
    $$\frac{{\large d} m_{PenI}}{d t} = (L_{lux} + \frac{\alpha_{lux}}{1+(\frac{K_{d2}}{luxR/AHL]_{2}})^{n_{lux}}} ) {\cdot} PenI_{gene} - d_{mPenI} {\cdot} {m_{PenI}} $$
+
−
    $$\frac{{\large d} CheZ}{d t} = \beta_{CheZ} {\cdot} {m_{CheZ}} - d_{CheZ} {\cdot} {CheZ} $$
+
−
    $$\frac{{\large d} PenI}{d t} = \beta_{PenI} {\cdot} {m_{PenI}} - d_{PenI} {\cdot} {PenI} $$
+
−
    $$\frac{{\large d} m_{RFP}}{d t} = (L_{Pen} + {\frac{\alpha_{Pen}}{1 + ({\frac{PenI}{K_{d3}}})^{n_{Pen}}}}) {\cdot} RFP_{gene} - d_{mRFP} {\cdot} m_{RFP} $$
+
−
    $$\frac{{\large d} RFP}{d t} = \beta_{RFP} {\cdot}{m_{RFP}} - d_{RFP} {\cdot}{RFP} $$
+
−
   
+
  
−
We visualize these ODE's in the Simbiology toolbox. This gives us the following diagrams:
+
<div class="whitespace">
−
</p>
+
</div>
−
<img id="simcellB" src="https://static.igem.org/mediawiki/2015/f/f7/KUL_IM_SIM_CB_TV1.png" alt="Cell B" style="width: 100%";style="height: 100%" onclick="bigImg(this)" onclick="normalImg(this)">
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<div class="subimg">
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<a href="https://2015.igem.org/Team:KU_Leuven/Research">
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<br>
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<img src="https://static.igem.org/mediawiki/2015/6/63/Wiki_Button_-_Research2.png" width="100%">
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</a>
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</div>
  
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<a class="example-image-link" href="https://static.igem.org/mediawiki/2015/a/af/KU_Leuven_plasmidA.png" data-lightbox="example-1"><img class="example-image" src="https://static.igem.org/mediawiki/2015/a/af/KU_Leuven_plasmidA.png" alt="plasmidA" height="100%" width="100%" onmouseover="Slave()"/></a>
+
<div class="whitespace">
 +
</div>
  
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<p>
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<div class="subimg">
−
Test test test test test ultra test
+
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
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</p>
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<img src="https://static.igem.org/mediawiki/2015/a/aa/Wiki_Button_-_Modelling2.png" width="100%">
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<a href="https://2015.igem.org/Team:KU_Leuven/Research/Idea" onmouseover="Vinnie()">To the lab!</a>
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<div class="subimg">
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<br>
+
<a href="https://2015.igem.org/Team:KU_Leuven/Team/Members">
−
<br>
+
<img src="https://static.igem.org/mediawiki/2015/2/23/KUL_Wiki_Button_-_Team.png" width="100%">
−
<p> This is the best website i have ever seen! </p>
+
</a>
−
<img src="https://abc.xyz/img/signature.jpg" height="100%" width="100%" onmouseover="Vinnie()">
+
</div>
−
<p> °CEO Alphabet, founder Google </p>
+
−
<img src="http://library.lehigh.edu/omeka/archive/files/677abdf878f4e465a080d8c1f3820128.jpg" height=200px width="100%" onmouseover="Vinnie()">
+
−
<p> °Founder of the United States of America </p>
+
  
−
<br>
+
<div class="whitespace">
−
<br>
+
</div>
−
<img src="https://www.cocacola.be/happy/Content/wallpapers/coke_wallpaper_desktop_02" height="100%" width="100%" onmouseover="Vinnie()">
+
  
 +
<div class="subimg">
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
 +
<img src="https://static.igem.org/mediawiki/2015/5/59/Wiki_Button_-_Notebook2.png" width="100%">
 +
</a>
 +
</div>
 +
</div>
  
−
<p>
+
<div class="subtextrow">
−
Test test test test test.
+
<div class="subtext">
−
<h2> To-Do List </h2>
+
<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
−
    <ul contenteditable="true">
+
<h2>Project</h2>
−
        <li> Break mechanical cab driver. </li>
+
<p>We decided to work on the fundamental mechanisms behind pattern formation. To achieve our goal, the link between wet lab and modeling will be crucial to the successful design of our experiments.
−
        <li> Drive to abandoned factory
+
<br/>
−
        <li> Watch video of self </li>
+
−
    </ul>
+
 
</p>
 
</p>
 +
</a>
 
</div>
 
</div>
 +
 +
<div class="whitespace">
 
</div>
 
</div>
  
−
<!------------------------------------------------------Parameters---------------------------------------------------------->
+
<div class="subtext">
−
<div class="summarytext1">  
+
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
−
<div class="part">
+
<h2>Research</h2>
−
      <h2> X. Parameters </h2>
+
<p> Each experimental step requires a theoretical background.  This background, the protocols and the results of our experiments can be found in this subsection.
−
    </div>
+
<br/>
−
 
+
</p>
−
    <div class="part">
+
</a>
 +
</div>
  
−
  <table style="width:100%">
+
<div class="whitespace">
−
    <tr>  <th>Parameter</th>    <th>Value</th>              <th>Unit</th>        <th>Source</th>  <th>Comment</th></tr>
+
−
    <tr>  <td>$D_a$</td>        <td>$0.072 \cdot 10^{-3}$</td>  <td>$cm^2/h$</td>  <td>following <sup><a href="#Woodward1995">[1]
+
−
    </a></sup> </td> <td> </td>    </tr>
+
−
    <tr>  <td>$D_b$</td>        <td>$2.376 \cdot 10^{-3}$</td>  <td>$cm^2/h$</td>  <td>following <sup><a href="#Woodward1995">[1]
+
−
    </a></sup></td>  <td> </td>  </tr>
+
−
    <tr>  <td>$D_r$</td>        <td>$26.46 \cdot 10^{-3}$</td> <td>$cm^2/h$</td>        <td> as found in <sup><a href="#Umecky2006">[6]</a></sup>
+
−
              </td>  <td> $298.2 K$ </td>  </tr> 
+
−
    <tr>  <td>$D_h$</td>        <td>$50 \cdot 10^{-3}$</td> <td>$cm^2/h$</td>        <td>from <sup><a href="#Ortiz">[3]
+
−
    </a></sup>  </td>  <td> </td> </tr>
+
−
    <tr>  <td>$K_{c}$</td>      <td>$8.5 \cdot 10^{-3}$</td>          <td>$cm^2/h$</td>      <td>guessed</td> <td> </td> </tr> 
+
−
    <tr>  <td>$\gamma$</td>      <td>$10^{-5}$</td>          <td>$h^{-1}$ </td>          <td>from <sup><a href="#Woodward1995">[1]
+
−
    </a></sup></td> <td> </td>    </tr>
+
−
    <tr>  <td>$k_p$</td>      <td>$1.0 \cdot 10^2$</td>          <td>$cl^{-1}$</td>    <td>from <sup><a href="#Woodward1995">[1]
+
−
    </a></sup></td>  <td> </td>  </tr>
+
−
    <tr>  <td>$k_h$</td>      <td>$17.9  \cdot 10^{-4}$</td>      <td>$fmol/h$</td>    <td>computed from <sup><a href="#Goryachev2006">[4]</a></sup> and <sup><a href="#Ishihama2008">[8]</a></sup> </td> <td> </td>  </tr>
+
−
    <tr>  <td>$k_r$</td>      <td>$5.4199\cdot 10^{-4}$</td>          <td>$fmol/h$</td>    <td>computed from <sup><a href="#Yu2014">[7]</a></sup> and <sup><a href="#Ishihama2008">[8]</a></sup>  </td>  <td> </td>  </tr>
+
−
  <tr>  <td>$k_{lossH}$</td>      <td>$1/48$</td>          <td>$h^{-1}$</td>    <td> from <sup><a href="#Schaefer2000">[5]</a></sup></td> <td>$ ph = 7$ </td>  </tr>
+
−
 
+
−
  <tr>  <td>$k_{lossR}$</td>      <td>$1/80$</td>          <td>$h^{-1}$</td>    <td>guessed</td> <td> </td>  </tr>
+
−
  </table>
+
−
 
+
−
<style type="text/css">
+
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.tg  {border-collapse:collapse;border-spacing:0;border-color:#aaa;border-width:1px;border-style:solid;}
+
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.tg td{font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:0px;overflow:hidden;word-break:normal;border-color:#aaa;color:#333;background-color:#fff;}
+
−
.tg th{font-family:Arial, sans-serif;font-size:14px;font-weight:normal;padding:10px 5px;border-style:solid;border-width:0px;overflow:hidden;word-break:normal;border-color:#aaa;color:#fff;background-color:#f38630;}
+
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.tg .tg-2e9h{font-weight:bold;text-decoration:underline}
+
−
.tg .tg-e3zv{font-weight:bold}
+
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.tg .tg-07dj{font-weight:bold;font-size:14px}
+
−
.tg .tg-z2zr{background-color:#FCFBE3}
+
−
.tg .tg-ugmw{background-color:#FCFBE3;font-weight:bold;text-decoration:underline}
+
−
@media screen and (max-width: 800px) {.tg {width: auto !important;}.tg col {width: auto !important;}.tg-wrap {overflow-x: auto;-webkit-overflow-scrolling: touch;}}</style>
+
−
<div class="tg-wrap"><table class="tg">
+
−
  <tr>
+
−
    <th class="tg-e3zv">Protein</th>
+
−
    <th class="tg-07dj">Translation rate (a.u.)</th>
+
−
    <th class="tg-07dj">Translation rate (1/s)</th>
+
−
  </tr>
+
−
  <tr>
+
−
    <td class="tg-z2zr">LuxI</td>
+
−
    <td class="tg-z2zr">261.13</td>
+
−
    <td class="tg-ugmw">0.016</td>
+
−
  </tr>
+
−
  <tr>
+
−
    <td class="tg-031e">LuxR</td>
+
−
    <td class="tg-031e">279.61</td>
+
−
    <td class="tg-2e9h">0.016</td>
+
−
  </tr>
+
−
  <tr>
+
−
    <td class="tg-z2zr">cI857</td>
+
−
    <td class="tg-z2zr">5695.79</td>
+
−
    <td class="tg-z2zr">0.35</td>
+
−
  </tr>
+
−
  <tr>
+
−
    <td class="tg-031e">Transaminase B</td>
+
−
    <td class="tg-031e">2195.1</td>
+
−
    <td class="tg-031e">0.13</td>
+
−
  </tr>
+
−
  <tr>
+
−
    <td class="tg-z2zr">Ag43-YFP</td>
+
−
    <td class="tg-z2zr">33.22</td>
+
−
    <td class="tg-z2zr">0.0020</td>
+
−
  </tr>
+
−
  <tr>
+
−
    <td class="tg-031e">PenI</td>
+
−
    <td class="tg-031e">6696.73</td>
+
−
    <td class="tg-031e">0.41</td>
+
−
  </tr>
+
−
  <tr>
+
−
    <td class="tg-z2zr">RFP</td>
+
−
    <td class="tg-z2zr">2604.51</td>
+
−
    <td class="tg-z2zr">0.16</td>
+
−
  </tr>
+
−
  <tr>
+
−
    <td class="tg-031e">CheZ-GFP</td>
+
−
    <td class="tg-031e">396.95</td>
+
−
    <td class="tg-031e">0.024</td>
+
−
  </tr>
+
−
</table></div>
+
 
</div>
 
</div>
 +
 +
<div class="subtext">
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
 +
<h2>Modeling</h2>
 +
<p>The modeling team fits models to the data obtained by the wet lab. Synergically, simulations from the cyber lab will aid tuning the experimental conditions that lead to the desirable patterns.
 +
<br/>
 +
</p>
 +
</a>
 
</div>
 
</div>
  
−
<br>
 
−
<br>
 
−
<br>
 
−
<br>
 
−
<br>
 
−
<br>
 
  
−
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−
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−
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−
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<!-- <a href="#cellB" onclick="document.getElementById('Easy').style.display='inline';
 
−
<!-- document.getElementById('Scientific').style.display='none';return false;"> New </a>
 
−
<!-- <a href="#" onclick="Check()"> Test </a>
 
−
<!-- <button onclick="exefunction()">Check value</button>
 
−
<!-- <button onclick="EasySwitch()"> EasySwitch </button>
 
  
−
<!------------------------------------------------------References---------------------------------------------------------->
+
<div class="whitespace">
−
<div class="summaryheader">
+
</div>
−
    <div class="summaryimg">
+
−
  <img src="https://static.igem.org/mediawiki/2015/e/eb/KU_Leuven_fossilBackground.png" width="100%">
+
−
  <div class="head">
+
−
      <h2> References </h2>
+
−
    </div>
+
−
  </div>
+
−
  </div>
+
−
<div class="summarytext2">
+
−
<div class="part">
+
−
  <p id="ref1">[1] <a href="http://www.sciencedirect.com/science/article/pii/S0006349595804005#" target="_blank"> Temporal Patterns Generated by Salmonella typhimurium, D. E. Woodward, R. Tyson, M. R. Myerscough, J. D. Murray, E. 0.Budrene,l and H. C.Berg , Biophysical Journal Volume 68 May 1995 2181-2189 </a></p>
+
  
−
<!------------------------------------------------------Source code files--------------------------------------------------->
+
<div class="subtext">
−
<!-- UNCOMMENT BEFORE THE WIKI-FREEZE.
+
<a href="https://2015.igem.org/Team:KU_Leuven/Team/Members">
−
<!--  <div class="summaryheader">
+
<h2>Team</h2>
−
<!--    <div class="summaryimg">
+
<p>Diverse with respect to thoughts, perspectives, nationalities and languages, yet bound together by our enthusiasm for science and research. Would you like to know more about us?
−
<!--  <img src="https://static.igem.org/mediawiki/2015/e/eb/KU_Leuven_fossilBackground.png" width="100%">
+
<br/>
−
<!--  <div class="head">
+
</p>
−
<!--      <h2> Source Code </h2>
+
</a>
−
<!--    </div>
+
</div>
−
<!--  </div>
+
−
<!--  </div>
+
−
<!-- <div class="summarytext3">
+
−
<!-- <div class="part">
+
−
<!--  <p id="source1">[1] <a href="https://2015.igem.org/wiki/index.php?title=Team:KU_Leuven/Modeling/1dsource"> 1D simulation
+
−
<!-- code</a></p>
+
−
<!--  <p id="source2">[1] <a href="https://2015.igem.org/wiki/index.php?title=Team:KU_Leuven/Modeling/1dsource"> 2D main </a></p>
+
−
<!-- </div>
+
−
<!-- </div>  
+
  
 +
<div class="whitespace">
 +
</div>
  
 +
<div class="subtext">
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
 +
<h2>Notebook</h2>
 +
<p>Many small steps need to be taken to achieve our goal. We like to keep you informed and welcome you to discover our newsfeed and history!
 +
<br/>
 +
</p>
 +
</a>
 +
</div>
  
−
<!--------------------------------------------------Foot don't touch!------------------------------------------------------>
+
</div>
 +
<div class="subimgreadmore">
 +
<div class="subimgrm">
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
 +
<div id="more1">
 +
<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="40%" width="85%" alt="Read more">
 +
</div>
 +
</a>
 +
</div>
  
 +
<div class="whitespace">
 +
</div>
  
−
<div class="subsections">
+
<div class="subimgrm">
−
<div class="subsectionwrapper">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
−
<div class="subimgrow">
+
<div id="more2" z-index="2">
−
<div class="subimg">
+
<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="40%" width="85%" alt="Read more">
−
<img src="https://static.igem.org/mediawiki/2015/9/98/HybridCover.png" width="100%">
+
</div>
 +
</a>
 
</div>
 
</div>
  
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</div>
 
</div>
  
−
<div class="subimg">
+
<div class="subimgrm">
−
<img src="https://static.igem.org/mediawiki/2015/d/d8/ContinuousModelCover.png" width="100%">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
 +
<div id="more3">
 +
<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="40%" width="85%" alt="Read more">
 +
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 +
</a>
 
</div>
 
</div>
  
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</div>
 
</div>
  
−
<div class="subimg">
+
<div class="subimgrm">
−
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Team/Members">
−
<!---<img src="https://static.igem.org/mediawiki/2015/2/2b/KU_Leuven_Monocotyl.jpg" width="100%" height="100%" >-->
+
<div id="more4">
 +
<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="40%" width="85%" alt="Read more">
 +
</div>
 
</a>
 
</a>
 
</div>
 
</div>
 +
 +
<div class="whitespace">
 
</div>
 
</div>
  
−
<div class="subtext">
+
<div class="subimgrm">
−
<h2>Hybrid model</h2>
+
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
−
<p>
+
<div id="more5">
−
Coming soon
+
<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="100%" width="85%" alt="Read more">
−
</p>
+
</div>
 +
</a>
 
</div>
 
</div>
  
−
<div class="whitespace">
 
 
</div>
 
</div>
  
−
<div class="subtext">
+
<div class="subimgrowm">
−
  <h2>Top model</h2>
+
<div class="subimgm">
−
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling/Top"> Read more!
+
  <b>Project</b>
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
 +
<img src="https://static.igem.org/mediawiki/2015/1/1a/KUL_Wiki_Button_-_Project.png" width="100%">
 
</a>
 
</a>
 
</div>
 
</div>
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</div>
 
</div>
  
−
<div class="subtext">
+
 
−
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
+
<div class="subtextm">
−
<h2>Back</h2>
+
<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
 +
<p style='text-align:left'>We decided to work on the fundamental mechanisms behind pattern formation. To achieve our goal, the link between wet lab and modeling will be crucial to the successful design of our experiments.
 +
</p>
 
</a>
 
</a>
 
</div>
 
</div>
 
</div>
 
</div>
 +
 +
<div class="subimgrowm">
 +
 +
<div class="subimgm">
 +
<b>Research</b>
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
 +
<img src="https://static.igem.org/mediawiki/2015/archive/c/ca/20150807120732%21KU_Leuven_Wiki_Button_-_Wetlab.png" width="100%">
 +
</a>
 
</div>
 
</div>
  
 +
<div class="whitespace">
 +
</div>
  
  
 +
<div class="subtextm">
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
 +
<p style='text-align:left'> Each experimental step requires a theoretical background.  This background, the protocols and the results of our experiments can be found in this subsection.
 +
<br/>
 +
</p>
 +
</a>
 +
</div>
  
 +
</div>
 +
<div class="subimgrowm">
  
−
<!--------------------------------------------------EasySwitch-------------------------------------------------------------->
+
<div class="subimgm">
−
<script language="javascript" type="text/javascript">
+
<b>Modeling</b>
−
function EasySwitch(){
+
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
−
var lckv= document.getElementById("EasySwitch").checked;
+
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−
if (lckv==true)
+
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−
{
+
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−
$('.easy').css('display', 'inline');
+
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+
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+
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+
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{
+
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+
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+
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+
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+
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}
+
  
 +
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 +
</div>
  
−
$( "#Introduction" ).mouseenter(function() {
 
−
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−
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−
{
 
−
      $("#Left1").show();
 
−
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−
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−
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−
    $("#Left1").hide();
 
−
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−
$( "#Introduction" ).mouseenter(function() {
+
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−
      $("#SwitchText").show();
+
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
−
});
+
<p>The modeling team fits models to the data obtained by the wet lab. Synergically, simulations from the cyber lab will aid tuning the experimental conditions that lead to the desirable patterns.
−
$( "#Introduction" ).mouseleave(function() {
+
</p>
−
    $("#SwitchText").hide();
+
</a>
−
});
+
</div>
−
</script>
+
  
−
<!-------------------------------------------Load Lightbox ----------------------------------------------------------------->
+
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−
<link rel="stylesheet" type="text/css"
+
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−
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+
−
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+
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<script type="text/javascript" src="http://yourjavascript.com/11518521655/lightbox.js"></script>
+
  
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+
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+
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−
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+
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+
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+
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+
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      'fitImagesInViewport' : true,
+
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+
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+
  
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<!-------------------------------------------Load mathJax related stuff----------------------------------------------------->
+
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−
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+
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Latest revision as of 00:35, 20 November 2015

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Our project

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Test test ultra test Patterns are fascinating, from the veins of a leaf to the stripes of a zebra. Patterns are found everywhere in nature, but how they are formed is not entirely clear. We, the KU Leuven iGEM 2015 team, decided to work on the fundamental mechanisms behind pattern formation. The way cells of multicellular organisms interact to generate a specific pattern has triggered our curiosity. Our mission is to create astonishing biological patterns with engineered bacteria on a petri dish to unravel the secrets of nature. We will design a ‘proof of principle’ which can form the basis for fundamental research.

Read more



A last message of the team

We are back from the Jamboree!!

We were very happy to present our results to the jury and we got a positive feedback:

First we won a gold medal!!

And we were even nominated for 4 prices in the overgrad section: Best Poster, Best Education and Public Engagement, Best Modeling and Best New Application Project in which we were the runner-up!

We were very happy with these results and want to thank everybody involved who helped us to achieve this! Thank you very much!!


Project

We decided to work on the fundamental mechanisms behind pattern formation. To achieve our goal, the link between wet lab and modeling will be crucial to the successful design of our experiments.

Research

Each experimental step requires a theoretical background. This background, the protocols and the results of our experiments can be found in this subsection.

Modeling

The modeling team fits models to the data obtained by the wet lab. Synergically, simulations from the cyber lab will aid tuning the experimental conditions that lead to the desirable patterns.

Team

Diverse with respect to thoughts, perspectives, nationalities and languages, yet bound together by our enthusiasm for science and research. Would you like to know more about us?

Notebook

Many small steps need to be taken to achieve our goal. We like to keep you informed and welcome you to discover our newsfeed and history!

Read more
Read more
Read more
Read more
Read more
Project

We decided to work on the fundamental mechanisms behind pattern formation. To achieve our goal, the link between wet lab and modeling will be crucial to the successful design of our experiments.

Research

Each experimental step requires a theoretical background. This background, the protocols and the results of our experiments can be found in this subsection.

Modeling

The modeling team fits models to the data obtained by the wet lab. Synergically, simulations from the cyber lab will aid tuning the experimental conditions that lead to the desirable patterns.

Team

Diverse with respect to thoughts, perspectives, nationalities and languages, yet bound together by our enthusiasm for science and research. Would you like to know more about us?

Notebook

Many small steps need to be taken to achieve our goal. We like to keep you informed and welcome you to discover our newsfeed and history!

Contact

Address: Celestijnenlaan 200G room 00.08 - 3001 Heverlee
Telephone n°: +32(0)16 32 73 19
Mail: igem@chem.kuleuven.be