Difference between revisions of "Team:SIAT-SCIE/Model"

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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<h1> Modeling</h1>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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<h3> Gold Medal Criterion #3</h3>
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To complete for the gold medal criterion #3, please describe your work on this page and fill out the description on your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>. To achieve this medal criterion, you must convince the judges that your team has gained insight into your project from modeling. You may not convince the judges if your model does not have an effect on your project design or implementation.
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Please see the <a href="https://2017.igem.org/Judging/Medals"> 2017 Medals Page</a> for more information.
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<h3>Best Model Special Prize</h3>
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To compete for the <a href="https://2017.igem.org/Judging/Awards">Best Model prize</a>, please describe your work on this page  and also fill out the description on the <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>. Please note you can compete for both the gold medal criterion #3 and the best model prize with this page.
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            <p style="font-family:'Avenir';font-size:23px">
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<br><br>
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                <img src="https://static.igem.org/mediawiki/2017/b/bb/SIAT-SCIE_modeling.png" alt="comic" />
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You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
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        </div>
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        <div id="content">
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            <h3 style="font-family:'Avenir';font-size:23px">Results</h3>
  
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            <table>
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                <tr>
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                    <th></th>
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                    <th style="text-align:center;font-family:'Avenir';font-size:23px">-IPTG</th>
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                    <th style="text-align:center;font-family:'Avenir';font-size:23px">+IPTG</th>
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                <tr>
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                    <th style="font-family:'Avenir';font-size:23px">Control</th>
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                    <td style="font-family:'Avenir';font-size:23px">3072</td>
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                    <td style="font-family:'Avenir';font-size:23px">4244</td>
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                </tr>
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                <tr>
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                    <th style="font-family:'Avenir';font-size:23px">UV 5s</th>
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                    <td style="font-family:'Avenir';font-size:23px">4/7(5.5)</td>
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                    <td style="font-family:'Avenir';font-size:23px">15/46(30.5)</td>
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                </tr>
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                <tr>
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                    <th style="font-family:'Avenir';font-size:23px">UV 10s</th>
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                    <td style="font-family:'Avenir';font-size:23px">1/7(4)</td>
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                    <td style="font-family:'Avenir';font-size:23px">11/22(16.5)</td>
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                </tr>
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            </table>
  
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            <p style="font-family:'Avenir';font-size:23px">
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<h5> Inspiration </h5>
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            So, overall we can see that the control groups have similar clone numbers, while the + IPTG group displays approximately 4 to 5 fold survivability. The induced Dsup protein can help the cell survive high radiation exposure.
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<p>
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            </p>
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Here are a few examples from previous teams:
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            <br />
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            <img src="https://static.igem.org/mediawiki/2017/e/e2/SIAT-SCIE_model1.jpg" alt="model1" style="width:1000px;margin-left:130px;"/>
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<ul>
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            <p style="font-family:'Avenir';font-size:23px">
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<li><a href="https://2016.igem.org/Team:Manchester/Model">Manchester 2016</a></li>
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            Due to the limited sample size, we are unable to conduct T-test or similar statistical tests on our data.
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">TU Delft 2016  </li>
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            </p>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
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            <br />
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
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            <p style="font-family:'Avenir';font-size:23px">
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            We have adopted a simpler model to investigate the correspondence between Dsup expression and survival rate.
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            </p>
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            <br />
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            <p style="font-family:'Avenir';font-size:23px">
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                Assume a pair of constants, representing the cell damage rate. (k1 and k2 for – IPTG and + IPTG groups)
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            </p>
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            <p style="font-family:'Avenir';font-size:23px">
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            Let the survival of cells be function S(t), given the cells are under UV light incidence,</p>
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            <img src="https://static.igem.org/mediawiki/2017/b/bc/SIAT-SCIE_model2.png" alt="model2" style="width:200px;margin-left:130px;"/>
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            <p style="font-family:'Avenir';font-size:23px">Solve the equation, we have,</p>
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            <img src="https://static.igem.org/mediawiki/2017/8/86/SIAT-SCIE_model3.png" alt="model3" style="width:200px;margin-left:130px;"/>
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          <p style="font-family:'Avenir';font-size:23px"> Put in the data, we have</p>
  
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            <img src="https://static.igem.org/mediawiki/2017/2/20/SIAT-SCIE_model4.png" alt="model4" style="width:1000px;margin-left:130px;"/>
  
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            <p style="font-family:'Avenir';font-size:23px">Solve differential equations in Mathematica, we have</p>
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            <p style="font-family:'Avenir';font-size:23px">
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            k1 = 1.26507</p>
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            <p style="font-family:'Avenir';font-size:23px">
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            k2 =0.95675
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                </p>
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            <p style="font-family:'Avenir';font-size:23px">
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            The Dsup increases the cell resilience to radiation about 25%.</p>
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            <p style="font-family:'Avenir';font-size:23px">
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            Extend time to 20s, we have the following expectations
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            </p>
  
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            <p style="font-family:'Avenir';font-size:23px">We noticed the model is somehow inaccurate after extending the UV time to 10s onwards, taking into account the sample size, this is what we can do.
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            </p>
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            <p style="font-family:'Avenir';font-size:23px">
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            A more accurate analysis is in the PDF file attached.
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            Another complete differential analysis is in another PDF down below.
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            </p>
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            <embed src="https://static.igem.org/mediawiki/2017/2/24/SIAT-SCIE_Model.pdf" alt="Modeling" />
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            <p style="font-family:'Avenir';text-align:center; font-size:23px; width:800px;margin-left:225px;color:blue;"><a href="https://static.igem.org/mediawiki/2017/2/24/SIAT-SCIE_Model.pdf" alt="DOWNLOAD PDF"><em>Donwload the pdf</em></a><p style="font-family:'Avenir';font-size:23px";>
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<p style="font-family:'Avenir';text-align:center; font-size:23px; width:800px;margin-left:225px;color:blue;"><a href="https://static.igem.org/mediawiki/2017/3/34/SIAT-SCIE_Modeling.pdf" alt="DOWNLOAD PDF"><em>Donwload an complete analysis</em></a><p style="font-family:'Avenir';font-size:23px";>
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{{SIAT-SCIE footer}}

Latest revision as of 03:46, 2 November 2017

comic

Results

-IPTG +IPTG
Control 3072 4244
UV 5s 4/7(5.5) 15/46(30.5)
UV 10s 1/7(4) 11/22(16.5)

So, overall we can see that the control groups have similar clone numbers, while the + IPTG group displays approximately 4 to 5 fold survivability. The induced Dsup protein can help the cell survive high radiation exposure.


model1

Due to the limited sample size, we are unable to conduct T-test or similar statistical tests on our data.


We have adopted a simpler model to investigate the correspondence between Dsup expression and survival rate.


Assume a pair of constants, representing the cell damage rate. (k1 and k2 for – IPTG and + IPTG groups)

Let the survival of cells be function S(t), given the cells are under UV light incidence,

model2

Solve the equation, we have,

model3

Put in the data, we have

model4

Solve differential equations in Mathematica, we have

k1 = 1.26507

k2 =0.95675

The Dsup increases the cell resilience to radiation about 25%.

Extend time to 20s, we have the following expectations

We noticed the model is somehow inaccurate after extending the UV time to 10s onwards, taking into account the sample size, this is what we can do.

A more accurate analysis is in the PDF file attached. Another complete differential analysis is in another PDF down below.

Donwload the pdf

Donwload an complete analysis




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