Difference between revisions of "Team:Shanghai Metro/Model"

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                    <a href="https://2021.igem.org/Team:Shanghai_Metro">Home</a>
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                    <a href="">Project</a>
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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 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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<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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<h3> Gold Medal Criterion #3</h3>
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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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Please see the <a href="https://2021.igem.org/Judging/Medals">2021 Medals Page</a> for more information.
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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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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 class="sub-title">MODEL</div>
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        <div class="article-content">In order to determine the appropriate tetracycline induction concentration range
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            for better growth of our
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            patent strains, we tested the OD<sub>600</sub> of the strains under various concentration of tetracycline
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            and collected
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            the data against hours and built the model.</div>
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        <div class="article-content">Below is the initial data:</div>
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        <div class="img-wrap">
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            <span>Table 1. OD<sub>600</sub> value of the strain D: Pus232-ike4-tke4 after 6 hours</span>
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            <img src="https://static.igem.org/mediawiki/2021/c/cd/T--Shanghai_Metro--model01.jpg" alt="" />
 +
        </div>
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        <div class="article-content">According to the scatter-plot analysis by MATLAB, the data points have a tendency
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            of oscillation decline,
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            and there is no model of elementary function conforming to this trend. Therefore, we decided to use
 +
            interpolation method to study the numerical transformation and obtained the final curve.</div>
 +
        <div class="article-content">Interpolation method selection: although the curve obtained by spline interpolation
 +
            (Spline) is the most smooth, it will produce negative values, which does not conform to the actual
 +
            situation. Therefore, Hermite interpolation method (Pchip) is chosen to keep the shape of the original data.
 +
        </div>
 +
        <div class="img-wrap">
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            <img src="https://static.igem.org/mediawiki/2021/2/21/T--Shanghai_Metro--chg2.jpg" alt="" />
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        </div>
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        <div class="article-content">As the curve above, the X-coordinate shows the concentration of tetracycline and
 +
            the Y-coordinate shows the corresponding OD<sub>600</sub> value of the strain D. In order to find the
 +
            appropriate range
 +
            of the tetracycline concentration, we referred the OD<sub>600</sub> value of the blank control strain after
 +
            6 hours
 +
            without tetracycline:</div>
 +
        <div class="img-wrap">
 +
            <span>Table 2. OD<sub>600</sub> value of the strain E: Pus232 after 6 hours</span>
 +
            <img src="https://static.igem.org/mediawiki/2021/6/6e/T--Shanghai_Metro--model03.jpg" alt="" />
 +
        </div>
 +
        <div class="article-content">Therefore we drew a horizontal line where OD<sub>600</sub> equals 0.3268 and find
 +
            the cross
 +
            points of these two lines where Xs are 17, 26, 78 and 113. As seen from the graph, it indicates that the
 +
            growth of our patent strain (strain D) could grow normally even better the normal strain (strain E) when we
 +
            add the tetracycline within the range from 17 µg/L to 26 µg/L, or the more recommended 78 µg/L to
 +
            113µg/L.Regarding the range from 0 to 17 µg/L where we didn't have samples to verify the accuracy, thus we
 +
            didn’t count it as the recommended concentration range.
 +
            To sum up, this model and this recommended concentration range could be used for the future application of
 +
            our patented-strain protection technology.</div>
 +
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Latest revision as of 03:01, 20 October 2021

Shanghai_Metro

MODEL
In order to determine the appropriate tetracycline induction concentration range for better growth of our patent strains, we tested the OD600 of the strains under various concentration of tetracycline and collected the data against hours and built the model.
Below is the initial data:
Table 1. OD600 value of the strain D: Pus232-ike4-tke4 after 6 hours
According to the scatter-plot analysis by MATLAB, the data points have a tendency of oscillation decline, and there is no model of elementary function conforming to this trend. Therefore, we decided to use interpolation method to study the numerical transformation and obtained the final curve.
Interpolation method selection: although the curve obtained by spline interpolation (Spline) is the most smooth, it will produce negative values, which does not conform to the actual situation. Therefore, Hermite interpolation method (Pchip) is chosen to keep the shape of the original data.
As the curve above, the X-coordinate shows the concentration of tetracycline and the Y-coordinate shows the corresponding OD600 value of the strain D. In order to find the appropriate range of the tetracycline concentration, we referred the OD600 value of the blank control strain after 6 hours without tetracycline:
Table 2. OD600 value of the strain E: Pus232 after 6 hours
Therefore we drew a horizontal line where OD600 equals 0.3268 and find the cross points of these two lines where Xs are 17, 26, 78 and 113. As seen from the graph, it indicates that the growth of our patent strain (strain D) could grow normally even better the normal strain (strain E) when we add the tetracycline within the range from 17 µg/L to 26 µg/L, or the more recommended 78 µg/L to 113µg/L.Regarding the range from 0 to 17 µg/L where we didn't have samples to verify the accuracy, thus we didn’t count it as the recommended concentration range. To sum up, this model and this recommended concentration range could be used for the future application of our patented-strain protection technology.

Contact Info.

Email: binghan423@163.com; runshigu@126.com

Wechat Official Account: IGEM VIPatent