Difference between revisions of "Team:Jilin China/Model"

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       <h2>Background</h2>
 
       <h2>Background</h2>
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       <p>We generated mathematical models of heat-inducible RNA-based thermosensors toolkit. The aim of our models was to build a SynRT toolkit for potential users and develop an intelligent system to screen valid thermosensors, which help the designers avoid the undesirable thermosensors.</p>
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       <p>Since RNA-based thermoregulation performs in a more immediate and more effective manner, we focused on building a RNA-based thermosensors toolkit. The principle of heat-inducible RNA-based thermosensors is when temperature increase, hydrogen bond fracture, and the secondary structure (stem-loop structure) of RNA thermosensors is destroyed. The RBS sequence exposes and fluorescence increases. However, lacking of a proven Toolkit hamper the heavy use of this kind of thermosensor. Our model is aiming at building a data base for our Toolkit with focused features for potential users.</p>
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      <p>We also created a model, which integrated with our HP group by calculating the Thermal Losses of fermentation cylinder. This model is aiming at estimating the cost saving and energy conservation of potential industry applications.</p>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/a/aa/T--Jilin_China--model--yht1.svg" width="70%"/></div>
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<p class="figure">Figure 1. principle of heat-inducible RNA-based thermosensors</p>
 
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     <li class="paragraph_2" id="paragraph_2">
 
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       <h2>Methodology</h2>
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       <h2>Achievement</h2>
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      <ul>
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      <li>Developed a Curve Fitting Model to extract focused feature of Themosensors.</li>
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      <li>Developed a quantitative criterion to judge an applicable thermosensor.</li>
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      <li>Developed an Intelligent Screening System to avoid undesirable thermosensors, improving our experimental efficiency.</li>
 +
      <li>Found free energy and GC content as crucial factor on RNA-based thermosensors.</li>
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      <li>Developed an Thermo Loss System to evaluate the cost effect of temperature.</li>
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      <li>Made our script publically available for use by other teams.</li>
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      </ul>
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    </div>
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    </li>
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    <li class="paragraph_2" id="paragraph_2">
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      <h2>Achievement</h2>
 
       <p>We employ numerous technics and equations to have the most accuracy access to the problems raised in our project. Examples include <b>random forest algorithm in machine learning</b>, <b>statistical postrulate</b>, <b>least square estimation</b>, <b>Taylor serious expansion</b>, <b>Van 't Hoff statistical</b> , <b>Hill equation</b>, <b>heat conduction equation</b> and <b>finite difference calculus</b>.</p>
 
       <p>We employ numerous technics and equations to have the most accuracy access to the problems raised in our project. Examples include <b>random forest algorithm in machine learning</b>, <b>statistical postrulate</b>, <b>least square estimation</b>, <b>Taylor serious expansion</b>, <b>Van 't Hoff statistical</b> , <b>Hill equation</b>, <b>heat conduction equation</b> and <b>finite difference calculus</b>.</p>
 
       <p>To see detailed information, please follow the links below models and have a try of our database!</p>
 
       <p>To see detailed information, please follow the links below models and have a try of our database!</p>

Revision as of 20:16, 17 October 2018

MODEL


Background Methodology Integration

Model

  • Background

    Since RNA-based thermoregulation performs in a more immediate and more effective manner, we focused on building a RNA-based thermosensors toolkit. The principle of heat-inducible RNA-based thermosensors is when temperature increase, hydrogen bond fracture, and the secondary structure (stem-loop structure) of RNA thermosensors is destroyed. The RBS sequence exposes and fluorescence increases. However, lacking of a proven Toolkit hamper the heavy use of this kind of thermosensor. Our model is aiming at building a data base for our Toolkit with focused features for potential users.

    Figure 1. principle of heat-inducible RNA-based thermosensors

  • Achievement

    • Developed a Curve Fitting Model to extract focused feature of Themosensors.
    • Developed a quantitative criterion to judge an applicable thermosensor.
    • Developed an Intelligent Screening System to avoid undesirable thermosensors, improving our experimental efficiency.
    • Found free energy and GC content as crucial factor on RNA-based thermosensors.
    • Developed an Thermo Loss System to evaluate the cost effect of temperature.
    • Made our script publically available for use by other teams.

  • Achievement

    We employ numerous technics and equations to have the most accuracy access to the problems raised in our project. Examples include random forest algorithm in machine learning, statistical postrulate, least square estimation, Taylor serious expansion, Van 't Hoff statistical , Hill equation, heat conduction equation and finite difference calculus.

    To see detailed information, please follow the links below models and have a try of our database!

    Experiment Switching Behavior Database of RT Toolkit Thermal Intelligent Screening System Data Focused feature of RNA Thermosensor Validity Index of RNA Thermosensor Feedback:Design of Experiment to get Screen RNA Sequence with High Validity Melting Temperature Human Practices Ask for melting temperature, relative intensity, sensitivity.

  • Integration

    Our models are closely interlinked with our project. Results of our model also feedback to our design and human practices work in several important ways. Some examples include:

    1.The Curve Fitting Model bridge the gap between experimental data and valid thermal features for potential users. It provided us a detailed and continuous description of behavior of our RNA thermosensor by fitting a temperature-dependent expression curve. Moreover, it provided us a quantitative criteria to judge a valid thermosensor.

    2.The Screening System is an intelligent machine learning system to screen the valid RNA sequence. Using the random forest algorithm, it feedback to the design by minimizing invalid samples.

    3.The Cost Analyses built a heat conduction equation to estimate the heat loss power of Yogurt fermenters, providing us an important commercial reference to learn the effect of our production on cost saving and energy conservation during the work of human practice.