Difference between revisions of "Team:SHSID/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://2021.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2021.igem.org/Judging/Awards"> award listed below</a>. </p>
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                    <a href="https://2021.igem.org/Team:SHSID">Home</a>
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                    <a href="">Project</a>
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                            <li><a href="https://2021.igem.org/Team:SHSID/Description"
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                                    class="sub-nav-74">Description</a></li>
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                            <li><a href="https://2021.igem.org/Team:SHSID/Experiments"
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                                    class="sub-nav-74">Experiments</a></li>
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                            <li><a href="https://2021.igem.org/Team:SHSID/Results" class="sub-nav-74">Results</a></li>
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                    <a href="https://2021.igem.org/Team:SHSID/Implementation">Implementation</a>
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                    <a href="#">Model</a>
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                                    Members</a></li>
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                            <li><a href="https://2021.igem.org/Team:SHSID/Attributions"
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                                    class="sub-nav-74">Attributions</a></li>
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                            <li><a href="https://2021.igem.org/Team:SHSID/Collaborations"
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        <div class="sub-title">Model</div>
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        <div class="article-content">First, we extract the fermentation test data of the engineered strain CSY1297 from
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            the Nature article. </div>
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        <div class="img-wrap no-margin">
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            <img src="https://static.igem.org/mediawiki/2021/d/dc/T--SHSID--Model01.png" alt="" />
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        </div>
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        <div class="article-content">Use computer modeling to get the simple linear regression shown in the figure 1.
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        </div>
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        <div class="img-wrap no-margin">
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            <img src="https://static.igem.org/mediawiki/2021/3/32/T--SHSID--Model02.jpg" alt="" />
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            <span>Figure1.</span>
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        </div>
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        <div class="article-content">Because we use low-density cell (LDC) fermentation in the laboratory, the obtained
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            OD600 range is between 0 and 2, while the model OD600 range is between 21 and 27. There is a huge difference
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            between the two and it is not suitable for predicting the fermentation performance of our strains. </div>
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        <div class="article-content">Then we extracted fermentation test data from the Nature Communications article.
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            The engineered bacterial strain constructed in this article is genetically the closest to our bacteria, and
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            the article uses the same LDC fermentation as ours. Data are as follows:</div>
  
  
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            <img src="https://static.igem.org/mediawiki/2021/7/74/T--SHSID--Model03.png" alt="" />
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        <div class="article-content">Use computer modeling to get the simple linear regression shown in the figure2.
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<h1> Modeling</h1>
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        </div>
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        <div class="img-wrap no-margin">
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of 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. </p>
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            <img src="https://static.igem.org/mediawiki/2021/e/ea/T--SHSID--Model04.jpg" alt="" />
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            <span>Figure 2</span>
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<p>Please note you can compete for both the Gold Medal criterion #3 and the Best Model prize with this page. </p>
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        </div>
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        <div class="article-content">The fit between the linear model and the data is low. After optimizing the
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</div>
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            parameters of the equation, we get the modified simple linear regression shown in the figure 3.</div>
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<div class="clear"></div>
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        <div class="img-wrap no-margin">
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            <img src="https://static.igem.org/mediawiki/2021/1/1e/T--SHSID--Model05.jpg" alt="" />
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<div class="column full_size">
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            <span>Figure 3.</span>
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<h3> Gold Medal Criterion #3</h3>
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        </div>
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<p>
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        <div class="article-content">The fit between modified simple linear model and the data is still low, so we get
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Use modeling to gain insight into how your project works or should be implemented. Explain your model's assumptions, data, parameters, and results in a way that anyone could understand.
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            the polynomial use to get the following model (figure 4).</div>
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<br><br>
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        <div class="img-wrap no-margin">
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Please see the <a href="https://2021.igem.org/Judging/Medals">2021 Medals Page</a> for more information.  
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            <img src="https://static.igem.org/mediawiki/2021/4/44/T--SHSID--Model06.jpg" alt="" />
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</p>
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            <span>Figure 4.</span>
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        </div>
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</div>
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        <div class="article-content">After furthering the possible parameters, we get the modified polynomial linear
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            regression shown in figure 5.</div>
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<div class="column two_thirds_size">
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        <div class="img-wrap no-margin">
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<h3>Best Model Special Prize</h3>
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            <img src="https://static.igem.org/mediawiki/2021/f/f1/T--SHSID--Model07.jpg" alt="" />
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            <span>Figure 5.</span>
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<p>Models and computer simulations provide a great way to describe the functioning and operation of BioBrick Parts and Devices. Synthetic biology is an engineering discipline and part of engineering is simulation and modeling to determine system behavior before building your design. 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 before or in conjunction with experiments in the wetlab.
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        </div>
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</p><p>
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        <div class="article-content">Continue to optimize, we get the polynomial linear regression-2 shown in figure 6.
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To compete for the <a href="https://2021.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://2021.igem.org/Judging/Judging_Form">judging form</a>.  
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        </div>
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</p>
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        <div class="img-wrap no-margin">
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            <img src="https://static.igem.org/mediawiki/2021/8/89/T--SHSID--Model08.jpg" alt="" />
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</div>
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            <span>Figure 6.</span>
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        </div>
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        <div class="article-content">The R-squared reaches 0.9855, which can be used to predict the performance of our
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<div class="column third_size">
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            engineered bacteria to produce tropine.
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<div class="highlight decoration_A_full">
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            Substituting the time and the OD600 value we tested in the laboratory into the model to get figures 7.
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<h3> Inspiration </h3>
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        </div>
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<p>You can look at what other teams did to get some inspiration! <br />
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        <div class="img-wrap no-margin">
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Here are a few examples:</p>
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            <img src="https://static.igem.org/mediawiki/2021/6/64/T--SHSID--Model09.jpg" alt="" />
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<ul>
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            <span>Figure 7.</span>
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<li><a href="https://2018.igem.org/Team:GreatBay_China/Model">2018 GreatBay China</a></li>
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        </div>
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<li><a href="https://2018.igem.org/Team:Leiden/Model">2018 Leiden</a></li>
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        <div class="article-content">The results show that when the OD600 of our engineered bacteria reaches a certain
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<li><a href="https://2019.igem.org/Team:IISER_Kolkata/Model">2019 IISER Kolkata</a></li>
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            value, the output of tropine will increase sharply, indicating that our engineered bacteria have great
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<li><a href="https://2019.igem.org/Team:Exeter/Model">2019 Exeter</li>
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            industrial application prospects.</div>
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<li><a href="https://2019.igem.org/Team:Mingdao/Model">2019 Mingdao</a></li>
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        <div class="article-title">Reference</div>
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<li><a href="https://2020.igem.org/Team:Harvard/Model">2020 Harvard</a></li>
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        <div class="article-content">
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<li><a href="https://2020.igem.org/Team:Leiden/Model">2020 Leiden</a></li>
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            1. Prashanth Srinivasan & Christina D. Smolke. Biosynthesis of medicinal tropane alkaloids in yeast.Nature |
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</ul>
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            Vol 585 | 24 September 2020 | 614-619 <br />
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</div>
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            2. Prashanth Srinivasan & Christina D. Smolke. Engineering a microbial biosynthesis platform for de novo
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</div>
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            production of tropane alkaloids.NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11588-w
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Latest revision as of 16:59, 19 October 2021

SHSID

Model
First, we extract the fermentation test data of the engineered strain CSY1297 from the Nature article.
Use computer modeling to get the simple linear regression shown in the figure 1.
Figure1.
Because we use low-density cell (LDC) fermentation in the laboratory, the obtained OD600 range is between 0 and 2, while the model OD600 range is between 21 and 27. There is a huge difference between the two and it is not suitable for predicting the fermentation performance of our strains.
Then we extracted fermentation test data from the Nature Communications article. The engineered bacterial strain constructed in this article is genetically the closest to our bacteria, and the article uses the same LDC fermentation as ours. Data are as follows:
Use computer modeling to get the simple linear regression shown in the figure2.
Figure 2
The fit between the linear model and the data is low. After optimizing the parameters of the equation, we get the modified simple linear regression shown in the figure 3.
Figure 3.
The fit between modified simple linear model and the data is still low, so we get the polynomial use to get the following model (figure 4).
Figure 4.
After furthering the possible parameters, we get the modified polynomial linear regression shown in figure 5.
Figure 5.
Continue to optimize, we get the polynomial linear regression-2 shown in figure 6.
Figure 6.
The R-squared reaches 0.9855, which can be used to predict the performance of our engineered bacteria to produce tropine. Substituting the time and the OD600 value we tested in the laboratory into the model to get figures 7.
Figure 7.
The results show that when the OD600 of our engineered bacteria reaches a certain value, the output of tropine will increase sharply, indicating that our engineered bacteria have great industrial application prospects.
Reference
1. Prashanth Srinivasan & Christina D. Smolke. Biosynthesis of medicinal tropane alkaloids in yeast.Nature | Vol 585 | 24 September 2020 | 614-619
2. Prashanth Srinivasan & Christina D. Smolke. Engineering a microbial biosynthesis platform for de novo production of tropane alkaloids.NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11588-w
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