Difference between revisions of "Team:BIT/Model"

 
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<li class="has-dropdown">
 
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<a>Project</a>
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<a style="color:#1b8fac">Project</a>
 
<ul class="dropdown">
 
<ul class="dropdown">
 
<li><a href="https://2017.igem.org/Team:BIT/Design">Design</a></li>
 
<li><a href="https://2017.igem.org/Team:BIT/Design">Design</a></li>
 
<li><a href="https://2017.igem.org/Team:BIT/Demonstrate">Demonstrate</a></li>
 
<li><a href="https://2017.igem.org/Team:BIT/Demonstrate">Demonstrate</a></li>
<li><a href="https://2017.igem.org/Team:BIT/model">Model</a></li>
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<li><a href="https://2017.igem.org/Team:BIT/Model">Model</a></li>
 
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<a href="https://2017.igem.org/Team:BIT/achievement">Achievement</a>
 
<a href="https://2017.igem.org/Team:BIT/achievement">Achievement</a>
 
<ul class="dropdown">
 
<ul class="dropdown">
<li><a href="https://2017.igem.org/Team:BIT/medal">Medal</a></li>
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<li><a href="https://2017.igem.org/Team:BIT/Medal">Medal</a></li>
<li><a href="2017.igem.org/Team:BIT/Prize">Prize</a></li>
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<li><a href="https://2017.igem.org/Team:BIT/Prize">Prize</a></li>
<li><a href="https://2017.igem.org/Team:BIT/part">Part</a></li>  
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<li><a href="https://2017.igem.org/Team:BIT/Parts">Part</a></li>  
                                                                         <li><a href="https://2017.igem.org/Team:BIT/design">Safety Form</a></li>
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                                                                         <li><a href="https://2017.igem.org/Team:BIT/https://2017.igem.org/Team:BIT/Safety">Safety Form</a></li>
 
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<li><a href="https://2017.igem.org/Team:BIT/HP/Silver">Silver</a></li>
 
<li><a href="https://2017.igem.org/Team:BIT/HP/Silver">Silver</a></li>
 
<li><a href="https://2017.igem.org/Team:BIT/HP/Gold_Integrated">Gold</a></li>
 
<li><a href="https://2017.igem.org/Team:BIT/HP/Gold_Integrated">Gold</a></li>
        <li><a href="https://2017.igem.org/Team:BIT/Model">Education & Public Engagement</a></li>
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        <li><a href="https://2017.igem.org/Team:BIT/Engagement"> Engagement</a></li>
                                                                 <li><a href="https://2017.igem.org/Team:BIT/Model">Entreperneurship</a></li>
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                                                                 <li><a href="https://2017.igem.org/Team:BIT/Entrepreneurship">Entreperneurship</a></li>
 
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<li class="has-dropdown">
 
<li class="has-dropdown">
<a href="https://2017.igem.org/Team:BIT/achievement">Notebook</a>
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<a href="https://2017.igem.org/Team:BIT/Notebook">Notebook</a>
 
<ul class="dropdown">
 
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<li><a href="https://2017.igem.org/Team:BIT/design">Gallery</a></li>
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<li><a href="https://2017.igem.org/Team:BIT/Gallery">Gallery</a></li>
<li><a href="2017.igem.org/Team:BIT/demonstrate">Track</a></li>
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<li><a href="https://2017.igem.org/Team:BIT/Track">Track</a></li>
<li><a href="https://2017.igem.org/Team:BIT/Model">Journal</a></li>
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<li><a href="https://2017.igem.org/Team:BIT/nb">Journal</a></li>
                                                                 <li><a href="https://2017.igem.org/Team:BIT/Model">Protocol</a></li>
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                                                                 <li><a href="https://2017.igem.org/Team:BIT/Protocol">Protocol</a></li>
 
</ul>
 
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                                                         <li class="has-dropdown">
<a href="https://2017.igem.org/Team:BIT/team">Team</a>
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<a href="https://2017.igem.org/Team:BIT/Team">Team</a>
 
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<li><a href="https://2017.igem.org/Team:BIT/design">Collarbration</a></li>
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<li><a href="https://2017.igem.org/Team:BIT/Collaborations">Collaborations</a></li>
<li><a href="2017.igem.org/Team:BIT/demonstrate">Member</a></li>
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<li><a href="https://2017.igem.org/Team:BIT/Team/Member">Member</a></li>
<li><a href="https://2017.igem.org/Team:BIT/Model">Attribution</a></li>
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<li><a href="https://2017.igem.org/Team:BIT/Attributions">Attributions</a></li>
 
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<div class="my-banner" id="top">
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<center><img src="https://static.igem.org/mediawiki/2017/6/69/BIT_Figure_MO3first.jpg" alt="" width="100%"><center>
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<div id="fh5co-blog">
 
<div class="container">
 
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<div class="col-md-8 col-md-offset-2 text-center fh5co-heading">
<h2>Journal</h2>
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<h1 style="color:#ffff01">Model</h1>
    <p>&nbsp;</p>
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<p><span class="label-warning"><font size=4><font color=black> March: </font> </font></span></p>
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<p><big>As for the meaning of the model, on the one hand our model can guide our team project, theoretically put forward the most scientific and reasonable program, and bring us inspiration to solve a variety of problems encountered in the work, which ensure the success of our project to achieve. On the other hand, The model can theoretically prove the feasibility and advantage of our project with the proving of Experiments, and fully expound our project.</big></p>
  </span><p>&nbsp;&nbsp;<br>
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<p><big> </big></p>
i. Week 1-2 (2017.03.04-2017.03.17)
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<p><big><b><i>What did our model achieve?</i></b></big></p>
  <br>
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<p> </p>
  &nbsp;&nbsp;&nbsp;
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<p><big>1. By establishing a mathematical model to describe the biochemical reaction process, the feasibility of the experimental target is verified.</big></p>
After discussion, the main goal of our project was to detect cancer of the liver by using small molecule
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<p><big>2. We put forward the model that characterizes the Target detectors with easily detectable substances by using biosensors.</big></p>
 +
<p><big>3. our project is intended to do the ultimate. Based on this ultimate goal, we need that there is a linear relationship between the direct test object and the target test object. So, we demonstrate and filter the tested substances that apply to our project through modeling.</big></p>
 +
<p><big>4. We use the laws of mass action, Milwaukee equation, Hill law and parameter relationship analysis, etc, to predict the results of biochemical reactions under different initial conditions, and achieve the purpose of the experimental guidance.</big></p>
 +
<p><big>5. We put forward to build dual fluorescent systems, in which two fluorescent proteins were introduced. We use the ratio of the two fluorescence values as the output signal, which play a role in the amplification of the input signal.</big></p>
 +
<p><big>6. We analyzed the promoter activity. And we evaluated and guided our gene line design.</big></p>
 +
<p><big>7. We use the law of mass action, Milwaukee equation, Hill law and parameter relationship analysis, etc., to predict the results of different initial conditions of biochemical reactions, to achieve the purpose of the experimental guide.</big></p>
 +
<p><big> </big></p>
 +
<p><big><b><i>What were we modeling?</i></b></big></p>
 +
<p> </p>
 +
<p><big>Our modeling is dedicated to verifying the feasibility of the experiment and guide our experiment.Our modeling will be divided into two large parts,namely Model of Biosensor and Model of Bioamplifier respectively.On the one hand, the modeling work of sensing part has an important guiding significance to biosensor experimental work and the whole project principle design. We have theoretically put forward the scientific and reasonable scheme, and have set out a goal and standard for other work in the team. project's design is based on insight we have gained from modeling. On the other hand, we have made an assessment of the whole of our project. As a project located in the diagnosis category, we use the model to predict the linear relationship between the material concentration, which is a good proof of our project is feasible, and has obvious advantages -- template.</big></p>
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<p><big> </big></p>
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<p><big> </big></p>
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<p><big><b><i>If you want to read more, please click:</i></b></big></p>
  
<br>
 
ii. Week 3 (2017.03.18-2017.03.24)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
After reviewing the literature, we chose lysine as our small molecule and chose lysine-deficient E.coli as our bacteria.
 
<br>
 
  
iii. week 4 (2017.03.25-2017.03.31)</span><br>
 
  &nbsp;&nbsp;&nbsp;
 
We chose our main experimental method.<br>
 
 
 
</p>
 
 
 
 
      <p>&nbsp;</p>
 
<p><span class="label-warning"><font size=4><font color=black> April: </font> </font></span></p>
 
  </span><p>&nbsp;&nbsp;<br>
 
i. Week 5 (2017.04.01-2017.04.07)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We listed the plasmids we might use, designed the gene lines, began to construct our part.
 
 
<br>
 
ii. Week 6 2017.04.08-2017.04.14)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We constructed our first part BBa_K2305008.
 
<br>
 
 
iii. Week 7 (2017.04.15-2017.04.21)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We constructed our part BBa_K2305011、BBa_K2305012 and BBa_K2305003、BBa_K2305002.<br>
 
 
 
iv.    Week 8 (2017.04.22-2017.04.28)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We import BBa_K876070 to E.coli, detect the growth and fluorescence curve of E.coil under various lysine concentration.<br>
 
</p>
 
 
 
      <p>&nbsp;</p>
 
<p><span class="label-warning"><font size=4><font color=black>May: </font> </font></span></p>
 
  </span><p>&nbsp;&nbsp;<br>
 
i. Week 9 (2017.04.29-2017.05.05)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We constructed BBa_K2305009、BBa_K2305010.
 
 
<br>
 
ii. Week 10 (2017.05.06-2017.05.12)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We constructed BBa_K2305014、BBa_K2305015、BBa_K2305016.
 
<br>
 
 
iii. Week 11 (2017.05.13-2017.05.19)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We constructed BBa_K2305007、BBa_K2305006.<br>
 
 
 
iv.    Week 12 (2017.05.20-2017.05.26)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We constructed BBa_K2305016、BBa_K2305005.<br>
 
v.    Week 13 (2017.05.27-2017.06.02)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We constructed BBa_K2305004、BBa_K2305013.<br>
 
</p>
 
 
 
      <p>&nbsp;</p>
 
<p><span class="label-warning"><font size=4><font color=black>June: </font> </font></span></p>
 
  </span><p>&nbsp;&nbsp;<br>
 
i. Week 14 (2017.06.03-2017.06.09)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We begin to detect the growth and fluorescence curve of E.coil which imported our plasmids.
 
 
<br>
 
ii. Week 15-17 (2017.06.10-2017.06.30)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We have achieved the detection of the growth and fluoresence curve of E.coli imported our plasmids.
 
<br>
 
</p>
 
 
 
      <p>&nbsp;</p>
 
<p><span class="label-warning"><font size=4><font color=black>July: </font> </font></span></p>
 
  </span><p>&nbsp;&nbsp;<br>
 
i. Week 18 (2017.07.01-2017.07.07)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We tried to knock out the lysa gene in E.coli by λRed recombination system.
 
 
<br>
 
ii. Week 19 ( 2017.07.08-2017.07.14)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We discussed about the problems we met in the gene-knocked.
 
<br>
 
 
iii. Week 20-21 (2017.07.15-2017.07.28)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We learned how to produce competent cells and produced enough cells..<br>
 
</p>
 
 
      <p>&nbsp;</p>
 
<p><span class="label-warning"><font size=4><font color=black>August: </font> </font></span></p>
 
  </span><p>&nbsp;&nbsp;<br>
 
i. Week 22-23 (2017.07.29-2017.08.16)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We import some plasmids we constructed to lysine-deficinent E.coli.
 
 
<br>
 
ii. Week 24-25 (  2017.08.12-2017.08.25)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We detect the growth and fluorescence curve of lysine-deficinent E.coli we had imported our plasmids.
 
<br>
 
 
iii. Week 26 (2017.08.26-2017.09.01)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
To achieve the standard of silver medal, we sorted out 19 parts completed in totally.<br>
 
</p>
 
 
      <p>&nbsp;</p>
 
<p><span class="label-warning"><font size=4><font color=black> September: </font> </font></span></p>
 
  </span><p>&nbsp;&nbsp;<br>
 
i. Week 27-28 (2017.09.02-2017.09.15)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
To reach the gold medal, we worked hard to improve an existing BioBrick, iGEM12_UT_Dallas’s BioBrick(BBa_K876070) and iGEM2006_Imperial’s BioBrick(BBa_J37032)
 
 
<br>
 
ii. Week 29-30 (  2017.09.16-2017.09.29)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
To achieve the standard of the copper medal, we have improved the characterizations of BBa_I13973、BBa_I6088、BBa_K584000、BBa_K876070
 
<br></p>
 
 
 
      <p>&nbsp;</p>
 
<p><span class="label-warning"><font size=4><font color=black>October: </font> </font></span></p>
 
  </span><p>&nbsp;&nbsp;<br>
 
i. Week 31-32 (2017.09.30-2017.10.13)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We sorted out our results and steps of the experiment.
 
 
<br>
 
ii. Week 33-34 (2017.10.14-2017.10.31)
 
<br>
 
  &nbsp;&nbsp;&nbsp;
 
We freeze-dried our plasmids and mailed it to IGEM, and then finished our wiki.
 
<br>
 
 
</p>
 
 
 
 
 
 
</div>
 
</div>
 
</div>
 
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                                            <img src="https://static.igem.org/mediawiki/2017/e/ec/BIT_Figure_About_The_Secondary_Structure_of_AP273.png" alt="Image" class="img-fluid tm-img">
<h2>Hire Us!</h2>
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                                            <figcaption>
<p>Facilis ipsum reprehenderit nemo molestias. Aut cum mollitia reprehenderit. Eos cumque dicta adipisci architecto culpa amet.</p>
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                                                <h2 class="tm-figure-title">Model<span>of</span> <span>Biosensor</span></h2>
<p><a href="#" class="btn btn-default btn-lg">Contact Us</a></p>
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                                                <a href="https://2017.igem.org/Team:BIT/MO1">View more</a>
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                                            </figcaption>         
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                                            <figcaption>
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                                                <h2 class="tm-figure-title">Model<span>of</span> <span>Bioamplifier</span></h2>
 +
                                             
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                                                <a href="https://2017.igem.org/Team:BIT/MO2">View more</a>
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          <h2>Contact Us!</h2>
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          <p><center>Please keep reading if you want to contact us.</center></p>
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          <h4>BIT</h4>
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          <p>It's an excellent Team with thoughtful persons full of funs to the academic</p>
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Latest revision as of 03:01, 2 November 2017

Model

As for the meaning of the model, on the one hand our model can guide our team project, theoretically put forward the most scientific and reasonable program, and bring us inspiration to solve a variety of problems encountered in the work, which ensure the success of our project to achieve. On the other hand, The model can theoretically prove the feasibility and advantage of our project with the proving of Experiments, and fully expound our project.

What did our model achieve?

1. By establishing a mathematical model to describe the biochemical reaction process, the feasibility of the experimental target is verified.

2. We put forward the model that characterizes the Target detectors with easily detectable substances by using biosensors.

3. our project is intended to do the ultimate. Based on this ultimate goal, we need that there is a linear relationship between the direct test object and the target test object. So, we demonstrate and filter the tested substances that apply to our project through modeling.

4. We use the laws of mass action, Milwaukee equation, Hill law and parameter relationship analysis, etc, to predict the results of biochemical reactions under different initial conditions, and achieve the purpose of the experimental guidance.

5. We put forward to build dual fluorescent systems, in which two fluorescent proteins were introduced. We use the ratio of the two fluorescence values as the output signal, which play a role in the amplification of the input signal.

6. We analyzed the promoter activity. And we evaluated and guided our gene line design.

7. We use the law of mass action, Milwaukee equation, Hill law and parameter relationship analysis, etc., to predict the results of different initial conditions of biochemical reactions, to achieve the purpose of the experimental guide.

What were we modeling?

Our modeling is dedicated to verifying the feasibility of the experiment and guide our experiment.Our modeling will be divided into two large parts,namely Model of Biosensor and Model of Bioamplifier respectively.On the one hand, the modeling work of sensing part has an important guiding significance to biosensor experimental work and the whole project principle design. We have theoretically put forward the scientific and reasonable scheme, and have set out a goal and standard for other work in the team. project's design is based on insight we have gained from modeling. On the other hand, we have made an assessment of the whole of our project. As a project located in the diagnosis category, we use the model to predict the linear relationship between the material concentration, which is a good proof of our project is feasible, and has obvious advantages -- template.

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