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

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<title> Ultra Test </title>
 
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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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    <h2> Internal Model </h2>
 
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<h3> Contact </h3>
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Address: Celestijnenlaan 200G room 00.08 - 3001 Heverlee<br>
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Telephone n°: +32(0)16 32 73 19<br>
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Mail: igem@chem.kuleuven.be<br> 
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      <a href=""><img src="https://static.igem.org/mediawiki/2015/1/15/KUL_Ko-Lo_Instruments_logo_transparant.png" alt="Ko-Lo Instruments" width="95%"></a>
 
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<div id="bioke">
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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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<div id="vwr">
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      <a href="http://www.gimv.com/en"><img src="https://static.igem.org/mediawiki/2015/a/ac/KU_Leuven_Logo_Gimv_Transparant.png" alt="Gimv" width="95%"></a>
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  <div id="machery">
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      <a href="http://www.filterservice.be/"><img src="https://static.igem.org/mediawiki/2015/4/41/KU_Leuven_Macherey_Nagel_logo_transparant.png" alt="Machery Nagel" width="95%"></a>
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      <a href="https://www.sigmaaldrich.com/belgium-nederlands.html"><img src="https://static.igem.org/mediawiki/2015/4/4b/KUL_Sigma-Aldrich_logo_transparant.png" alt="Sigma-Aldrich" width="95%"></a>
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    <div id="egilabo">
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      <a href="http://www.egilabo.be/"><img src="https://static.igem.org/mediawiki/2015/e/e9/KUL_Egilabo_logo_transparant.png" alt="Egilabo" width="95%"></a>
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<!------------------------------------------------------Begin Content------------------------------------------------------->
 
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<div id="center">
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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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<div id="pagetitle">
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    <label class="onoffswitch-label" for="EasySwitch">
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<h2>Our project</h2>
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        <span class="onoffswitch-inner" title="Press me please"></span>
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        <span class="onoffswitch-switch" title="Press me please"></span>
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    </label>
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<div class="scientific">
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<div id="scrolldown" class="center">
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<h3> 0.5 Test </h3>
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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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<p> This is a very difficult text.
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</p>
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<div class="easy">
 
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<h3> 0.5 Test </h3>
 
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<p> This is a very easy text. </p>
 
 
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<div id="VincentEaster" style="display: none">
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<div id="summarylogos">
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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 id="summarylogotwitter">
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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> 
 
</div>
 
</div>
  
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<div id="Left1" class="easyleft">
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<div id="summarylogofacebook">
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<p>En alle beelden op tv<br/>
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<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>
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Van bloed en oorlog om ons heen<br/>
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Werken daar ook niet echt aan mee</p>
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<div id="summarylogomail">
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<h2> 1. Introduction </h2>
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<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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<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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    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="Simbiology" class="scientific">
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<h2> 2. Simbiology </h2>    
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<div class="summary">
 
<p>
 
<p>
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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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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>
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<br>
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<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>
 
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<h2> 2.1 Cell A </h2>
 
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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>
 
<br>
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${\alpha}$:transcription term, ${\beta}$:translation term, ${d}$:degradation term, ${D}$:diffusion term
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<div id="VincentEaster" style="display: none">
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${K_d}$:dissociation constant, ${n}$:hill coefficient, ${L}$:leak term
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<img id="Cat" src="http://www.troll.me/images/science-cat/happy-birthday-from-science-cat-thumb.jpg" height="100%" width="100%">
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<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()">
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    $$\frac{{\large d} m_{cI}}{d t} = \alpha_1 {\cdot} cI_{gene} - d_{mCI} {\cdot} m_{cI}$$
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</div>
−
    $$\frac{{\large d}{cI}}{d t} = \beta_{cI} {\cdot} {cI} -2 {\cdot} {k_{cI,dim}} {\cdot} {cI}^2 + 2 {\cdot}{k_{-cI,dim}}{\cdot} {[cI]_2} - d_{cI} {\cdot} {cI}$$
+
−
    $$\frac{{\large d}{[cI]_2}}{d t}= k_{cI,dim} {\cdot} {cI}^2 - {k_{-cI,dim}}{\cdot} {[cI]_2} $$
+
−
    $$\frac{{\large d} m_{LuxI}}{d t} = (L_{lambda} + {\frac{\alpha_{lambda}}{1 + ({\frac{[cI]_2}{K_{d1}}})^{n_{cI}}}}) {\cdot} LuxI_{gene} - d_{mLuxI} {\cdot} m_{LuxI} $$
+
−
    $$\frac{{\large d} m_{LuxR}}{d t} = (L_{lambda} + {\frac{\alpha_{lambda}}{1 + ({\frac{[cI]_2}{K_{d1}}})^{n_{cI}}}}) {\cdot} LuxR_{gene} - d_{mLuxR} {\cdot} m_{LuxR} $$
+
−
    $$\frac{{\large d} LuxI}{d t} = \beta_{LuxI} {\cdot} {m_{LuxI}} - d_{LuxI} {\cdot}{LuxI} $$
+
−
    $$\frac{{\large d} LuxR}{d t} = \beta_{LuxR} {\cdot} {m_{LuxR}} -k_{lux,as} {\cdot}{LuxR}{\cdot}{AHL_{in}} + k_{lux,dis}{\cdot}{[LuxR/AHL]} - d_{LuxR} {\cdot}{LuxR} $$
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−
    $$\frac{{\large d} AHL_{in}}{d t} = {k_{luxI}} {\cdot} {luxI} - k_{lux,as} {\cdot}{luxR}{\cdot}{AHL_{in}} + k_{lux,dis}{\cdot}{[luxR/AHL]}+ ( {D_{IN,AHL}} {\cdot} {AHL_{out}} - {D_{OUT,AHL}} {\cdot} {AHL_{in}} ) - d_{AHL,in} {\cdot} {AHL_{in}}$$
+
−
    $$\frac{{\large d} AHL_{out}}{d t} = ( {D_{OUT,AHL}} {\cdot} {AHL_{in}} - {D_{IN,AHL}}{\cdot}{AHL_{out}} ) -d_{AHL,out}{\cdot}{AHL_{out}}$$
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−
    $$\frac{{\large d} [luxR/AHL]}{d t} = k_{lux,as} {\cdot}{luxR}{\cdot}{AHL_{in}} - k_{lux,dis}{\cdot}{[luxR/AHL]} - 2 {\cdot} k_{lux,dim} {\cdot}{[luxR/AHL]^2} + 2 {\cdot}{k_{-lux,dim}}{\cdot}{[luxR/AHL]_{2}}$$
+
−
    $$\frac{{\large d} [luxR/AHL]_{2}}{d t} = k_{lux,dim} {\cdot}{[luxR/AHL]^2} - k_{- lux,dim} {[luxR/AHL]} $$
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−
    $$\frac{{\large d} m_{ilvE}}{d t} = (L_{lux} + \frac{\alpha_{lux}}{1+(\frac{K_{d2}}{[luxR/AHL]_{2}})^{n_{lux}}} ) {\cdot} ilvE_{gene} - d_{milvE} {\cdot} {m_{ilvE}} $$
+
−
    $$\frac{{\large d} m_{Ag43}}{d t} = (L_{lux} + \frac{\alpha_{lux}}{1+(\frac{K_{d2}}{luxR/AHL]_{2}})^{n_{lux}}} ) {\cdot} Ag43_{gene} - d_{mAg43} {\cdot} {m_{Ag43}} $$
+
−
    $$\frac{{\large d} Transaminase B}{d t} = \beta_{TB} {\cdot} {m_{ilvE}} - d_{TB} {\cdot} {Transaminase B} $$
+
−
    $$\frac{{\large d} Leucine_{out}}{d t} = (D_{OUT,Leu} {\cdot}{leucine_{in}} - D_{IN,Leu} {\cdot}{leucine_{out}}) - d_{Leu,out} {\cdot} {Leucine_{out}} $$
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    $$\frac{{\large d} Ag43}{d t} = \beta_{Ag43} {\cdot} {m_{Ag43}} - d_{Ag43} {\cdot} {Ag43} $$
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<div class="subimg">
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<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
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<img src="https://static.igem.org/mediawiki/2015/1/1a/KUL_Wiki_Button_-_Project.png" width="100%">
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We visualize these ODE's in Simbiology which results in the following diagram:
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+
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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)">
+
<div class="subimg">
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
 +
<img src="https://static.igem.org/mediawiki/2015/6/63/Wiki_Button_-_Research2.png" width="100%">
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<h2> 2.1 Cell B </h2>
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 +
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We can repeat this assignment for Cell B:
+
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$$\frac{{\large d} m_{cI}}{d t} = \alpha_1 {\cdot} cI_{gene} - d_1 {\cdot} m_{cI}$$
+
−
    $$\frac{{\large d}{cI}}{d t} = \beta_1 {\cdot} {cI} -2 {\cdot} {k_{cI,dim}} {\cdot} {cI}^2 + 2 {\cdot}{k_{-cI,dim}}{\cdot} {[cI]_2} - d_{cI} {\cdot} {cI}$$
+
−
    $$\frac{{\large d}{[cI]_2}}{d t}= k_{cI,dim} {\cdot} {cI}^2 - {k_{-cI,dim}}{\cdot} {[cI]_2} $$
+
−
    $$\frac{{\large d} m_{luxR}}{d t} = (L_{lambda} + {\frac{\alpha_{lambda}}{1 + ({\frac{cI}{K_{d1}}})^{n_{cI}}}}) {\cdot} luxR_{gene} - d_{mluxR} {\cdot} m_{luxR} $$
+
−
    $$\frac{{\large d} luxR}{d t} = \beta_{luxR} {\cdot} {m_{luxR}} - d_{luxR} {\cdot}{luxR} $$
+
−
    $$\frac{{\large d} AHL_{in}}{d t} = ( {D_{IN,AHL}} {\cdot} {AHL_{out}} - {D_{OUT,AHL}} {\cdot} {AHL_{in}} ) - k_{lux,as}{\cdot}{luxR}{\cdot}{AHL_{in}} + k_{lux,dis}{\cdot}{[luxR/AHL]} - d_{AHL,in} {\cdot} {AHL_{in}} $$
+
−
    $$\frac{{\large d} AHL_{out}}{d t} = ( {D_{OUT,AHL}} {\cdot} {AHL_{in}} - {D_{IN,AHL}}{\cdot}{AHL_{out}} ) -d_{AHL,out}{\cdot}{AHL_{out}} $$
+
−
    $$\frac{{\large d} [luxR/AHL]}{d t} = k_{lux,as} {\cdot}{luxR}{\cdot}{AHL_{in}} - k_{lux,dis}{\cdot}{[luxR/AHL]} - 2 {\cdot} k_{lux,dim} {\cdot}{[luxR/AHL]^2} + 2 {\cdot}{[luxR/AHL]_{2}} $$
+
−
    $$\frac{{\large d} [luxR/AHL]_{2}}{d t} = k_{lux,dim} {\cdot}{[luxR/AHL]^2} - k_{- lux,dim} {[luxR/AHL]} $$
+
−
    $$\frac{{\large d} m_{CheZ}}{d t} = (L_{lux} + \frac{\alpha_{lux}}{1+(\frac{K_{d2}}{[luxR/AHL]_{2}})^{n_{lux}}} ) {\cdot} CheZ_{gene} - d_{mCheZ} {\cdot} {m_{CheZ}} $$
+
−
    $$\frac{{\large d} m_{PenI}}{d t} = (L_{lux} + \frac{\alpha_{lux}}{1+(\frac{K_{d2}}{luxR/AHL]_{2}})^{n_{lux}}} ) {\cdot} PenI_{gene} - d_{mPenI} {\cdot} {m_{PenI}} $$
+
−
    $$\frac{{\large d} CheZ}{d t} = \beta_{CheZ} {\cdot} {m_{CheZ}} - d_{CheZ} {\cdot} {CheZ} $$
+
−
    $$\frac{{\large d} PenI}{d t} = \beta_{PenI} {\cdot} {m_{PenI}} - d_{PenI} {\cdot} {PenI} $$
+
−
    $$\frac{{\large d} m_{RFP}}{d t} = (L_{Pen} + {\frac{\alpha_{Pen}}{1 + ({\frac{PenI}{K_{d3}}})^{n_{Pen}}}}) {\cdot} RFP_{gene} - d_{mRFP} {\cdot} m_{RFP} $$
+
−
    $$\frac{{\large d} RFP}{d t} = \beta_{RFP} {\cdot}{m_{RFP}} - d_{RFP} {\cdot}{RFP} $$
+
−
   
+
  
−
We visualize these ODE's in the Simbiology toolbox. This gives us the following diagrams:
+
<div class="subimg">
−
</p>
+
<a href="https://2015.igem.org/Team:KU_Leuven/Team/Members">
−
<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)">
+
<img src="https://static.igem.org/mediawiki/2015/2/23/KUL_Wiki_Button_-_Team.png" width="100%">
 +
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 +
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−
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+
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+
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<br>
+
  
−
<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="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>
 +
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 +
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−
<p>
+
<div class="subtextrow">
−
Test test test test test ultra test
+
<div class="subtext">
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
 +
<h2>Project</h2>
 +
<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.
 +
<br/>
 
</p>
 
</p>
−
<br>
+
</a>
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<br>
+
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<br>
+
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<a class="example-image-link" href="https://static.igem.org/mediawiki/2015/d/d6/KU_Leuven_plasmidB.png" data-lightbox="example-1"><img class="example-image" src="https://static.igem.org/mediawiki/2015/d/d6/KU_Leuven_plasmidB.png" alt="plasmidB" height="100%" width="100%" onmouseover="Slave()"/></a>
+
  
−
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+
<div class="whitespace">
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+
</div>
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<br>
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<a href="https://2015.igem.org/Team:KU_Leuven/Research/Idea" onmouseover="Vinnie()">To the lab!</a>
+
  
−
<br>
+
<div class="subtext">
−
<br>
+
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
−
<br>
+
<h2>Research</h2>
−
<p> This is the best website i have ever seen! </p>
+
<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.
−
<img src="https://abc.xyz/img/signature.jpg" height="100%" width="100%" onmouseover="Vinnie()">
+
<br/>
−
<p> °CEO Alphabet, founder Google </p>
+
</p>
−
<img src="http://library.lehigh.edu/omeka/archive/files/677abdf878f4e465a080d8c1f3820128.jpg" height=200px width="100%" onmouseover="Vinnie()">
+
</a>
−
<p> °Founder of the United States of America </p>
+
</div>
−
 
+
−
<br>
+
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<br>
+
−
<img src="https://www.cocacola.be/happy/Content/wallpapers/coke_wallpaper_desktop_02" height="100%" width="100%" onmouseover="Vinnie()">
+
  
 +
<div class="whitespace">
 +
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−
<p>
+
<div class="subtext">
−
Test test test test test.
+
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
−
<h2> To-Do List </h2>
+
<h2>Modeling</h2>
−
    <ul contenteditable="true">
+
<p style='text-align:left'>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.
−
        <li> Break mechanical cab driver. </li>
+
<br/>
−
        <li> Drive to abandoned factory
+
−
        <li> Watch video of self </li>
+
−
    </ul>
+
 
</p>
 
</p>
−
</div>
+
</a>
 
</div>
 
</div>
  
−
<!------------------------------------------------------Parameters---------------------------------------------------------->
 
−
<div class="summarytext1"> 
 
−
<div class="part">
 
−
      <h2> X. Parameters </h2>
 
−
    </div>
 
  
−
    <div class="part">
 
  
−
  <table style="width:100%">
+
<div class="whitespace">
−
    <tr>  <th>Parameter</th>    <th>Value</th>              <th>Unit</th>        <th>Source</th>  <th>Comment</th></tr>
+
</div>
−
    <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>
+
<div class="subtext">
−
  </table>  
+
<a href="https://2015.igem.org/Team:KU_Leuven/Team/Members">
 +
<h2>Team</h2>
 +
<p style='text-align:left'>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?
 +
<br/>
 +
</p>
 +
</a>
 +
</div>
  
−
<style type="text/css">
+
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.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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+
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+
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    <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>
+
 
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</div>
 +
 +
<div class="subtext">
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
 +
<h2>Notebook</h2>
 +
<p style='text-align:left'>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>
 
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+
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+
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+
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+
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−
<br>
+
<div id="more1">
−
<br>
+
<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>
  
−
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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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+
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+
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<!-- document.getElementById('Scientific').style.display='none';return false;"> New </a>
+
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+
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<!-- <button onclick="exefunction()">Check value</button>
+
−
<!-- <button onclick="EasySwitch()"> EasySwitch </button>
+
  
−
<!------------------------------------------------------References---------------------------------------------------------->
+
<div class="subimg">
−
<div class="summaryheader">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
−
    <div class="summaryimg">
+
<div id="more2" z-index="2">
−
  <img src="https://static.igem.org/mediawiki/2015/e/eb/KU_Leuven_fossilBackground.png" width="100%">
+
<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="40%" width="85%" alt="Read more">
−
  <div class="head">
+
</div>
−
      <h2> References </h2>
+
</a>
−
    </div>
+
</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>
+
  
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<!------------------------------------------------------Source code files--------------------------------------------------->
+
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+
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+
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+
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+
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+
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<!--  <p id="source1">[1] <a href="https://2015.igem.org/wiki/index.php?title=Team:KU_Leuven/Modeling/1dsource"> 1D simulation
+
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+
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+
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<!-- </div>
+
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+
  
 +
<div class="subimg">
 +
<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">
 +
</div>
 +
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 +
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 +
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<!--------------------------------------------------Foot don't touch!------------------------------------------------------>
 
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−
<img src="https://static.igem.org/mediawiki/2015/9/98/HybridCover.png" width="100%">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Team/Members">
 +
<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">
 +
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+
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
 +
<div id="more5">
 +
<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="100%" width="85%" alt="Read more">
 +
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Address: Celestijnenlaan 200G room 00.08 - 3001 Heverlee<br>
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Revision as of 10:33, 9 September 2015

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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




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