Difference between revisions of "Team:Vilnius-Lithuania/Model"

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       <p>The primary aim of this model was to identify parameters leading to rapidly-achieved and consistently high levels of BamA under conditions of co-expression of BamA, OmpA, and lgA. Prior to this it was important to identify particular parameters leading to these conditions and to examine some general trends. The number of molecules of mRNA and protein for each average, minimum and maximum plot and each of BamA, OmpA, and lgA after 2 hours were calculated (Fig.  3) and summarized (Tab.  3).</p>
 
       <p>The primary aim of this model was to identify parameters leading to rapidly-achieved and consistently high levels of BamA under conditions of co-expression of BamA, OmpA, and lgA. Prior to this it was important to identify particular parameters leading to these conditions and to examine some general trends. The number of molecules of mRNA and protein for each average, minimum and maximum plot and each of BamA, OmpA, and lgA after 2 hours were calculated (Fig.  3) and summarized (Tab.  3).</p>
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<div class="image-container"><img src="https://static.igem.org/mediawiki/2018/6/6d/T--Vilnius-Lithuania--_Fig3.1_Edinburgh_Model.png"></div>
 
<div class="image-container"><img src="https://static.igem.org/mediawiki/2018/6/6d/T--Vilnius-Lithuania--_Fig3.1_Edinburgh_Model.png"></div>
 
<div class="image-container"><img src="https://static.igem.org/mediawiki/2018/9/94/T--Vilnius-Lithuania--_Fig3.2_Edinburgh_Model.png">
 
<div class="image-container"><img src="https://static.igem.org/mediawiki/2018/9/94/T--Vilnius-Lithuania--_Fig3.2_Edinburgh_Model.png">
  
<strong>Fig. 3</strong> Minimum, maximum and average levels of mRNAs and protein for BamA, OmpA and lgA</p></div>
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<p><strong>Fig. 3</strong> Minimum, maximum and average levels of mRNAs and protein for BamA, OmpA and lgA</p></div>
 
<p></p>
 
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<strong>Tab. 3</strong>Average, minimum and maximum number of protein molecules after 2 hours'
 
<strong>Tab. 3</strong>Average, minimum and maximum number of protein molecules after 2 hours'
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<p>Fourier Amplitude Sensitivity Testing (FAST) indices represent the proportion of the output variance of the model attributable  to a particular variable and its interactions. Focusing on BamA expression as the protein of interest, total order FAST sensitivity indices were calculated using the BamA protein level each 20 minutes as the model output (Fig.  4).</p>
 
<p>Fourier Amplitude Sensitivity Testing (FAST) indices represent the proportion of the output variance of the model attributable  to a particular variable and its interactions. Focusing on BamA expression as the protein of interest, total order FAST sensitivity indices were calculated using the BamA protein level each 20 minutes as the model output (Fig.  4).</p>
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     <div class="image-container"><img src="https://static.igem.org/mediawiki/2018/4/4b/T--Vilnius-Lithuania--_Fig4_Edinburgh_Model.png">
 
     <div class="image-container"><img src="https://static.igem.org/mediawiki/2018/4/4b/T--Vilnius-Lithuania--_Fig4_Edinburgh_Model.png">
  
<strong>Fig. 4 </strong>FAST sensitivity analysis of BamA</p></div>
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<p><strong>Fig. 4 </strong>FAST sensitivity analysis of BamA</p></div>
 
<p>As it can be seen from the graph, number of BamA plasmid copies contributes most to output variance over the whole time span. Also, BamA mRNA degradation rate is considerably faster than BamA degradation rate - with mRNA halflife of the order of minutes and protein halflife of the order of hours - hence the greater FAST index.</p>
 
<p>As it can be seen from the graph, number of BamA plasmid copies contributes most to output variance over the whole time span. Also, BamA mRNA degradation rate is considerably faster than BamA degradation rate - with mRNA halflife of the order of minutes and protein halflife of the order of hours - hence the greater FAST index.</p>
 
<p></p>
 
<p></p>

Revision as of 20:11, 7 November 2018

Modeling

Mathematical model

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

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