http://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&feed=atom&action=historyTeam:Peking/Modeling - Revision history2024-03-28T13:25:38ZRevision history for this page on the wikiMediaWiki 1.16.5http://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&diff=205361&oldid=prevLgdeer: /* Introduction */2010-10-28T02:22:18Z<p><span class="autocomment">Introduction</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Introduction=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Introduction=</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The biological systems are full of noises, and the response of bioreporters <del class="diffchange diffchange-inline">represents </del>a Hill Function. Noises will be significantly amplified and the output detected will be invalid at the ends of dose response curve.(Figure 1(a)) Therefore, The detection is limited at a narrow range. In order to solve the problem, we seek to transform the Hill Function curve to a straight line. As Figure 1(a) shows, the noise is reducted, and the sensitivity and detectable-range-characteristic of biosensors will be significantly improved. <br><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The biological systems are full of noises, and the response of bioreporters <ins class="diffchange diffchange-inline">can be represented by </ins>a Hill Function. Noises will be significantly amplified and the output detected will be invalid at the ends of dose response curve.(Figure 1(a)) Therefore, The detection is limited at a narrow range. In order to solve the problem, we seek to transform the Hill Function curve to a straight line. As Figure 1(a) shows, the noise is reducted, and the sensitivity and detectable-range-characteristic of biosensors will be significantly improved. <br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Aimed at finding a genetic circuit that can perform the transformation, a simple and universal one for practice convenience, we adopted the process of [[Team:Peking/Notebook/Vocabulary#Reverse engineering|Reverse engineering]] which in our work means to enumerate all possible networks and analyzed whether they function well, thus getting the right topology. In details, we first express the target functionalities in quantitative characters and set numerical standards according to our expectations, next define the network for simplest circuit search and derive equations precisely describing it, then calculate the characters using the equations and compare them with standards, then further analyze the comparison results and find the simplest functional network. Finally, to fully understand it and provide enough information for application, we analyze the mechanism and the parameter preferences, as well as exploring whether the very circuit is necessary for performing the function well.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Aimed at finding a genetic circuit that can perform the transformation, a simple and universal one for practice convenience, we adopted the process of [[Team:Peking/Notebook/Vocabulary#Reverse engineering|Reverse engineering]] which in our work means to enumerate all possible networks and analyzed whether they function well, thus getting the right topology. In details, we first express the target functionalities in quantitative characters and set numerical standards according to our expectations, next define the network for simplest circuit search and derive equations precisely describing it, then calculate the characters using the equations and compare them with standards, then further analyze the comparison results and find the simplest functional network. Finally, to fully understand it and provide enough information for application, we analyze the mechanism and the parameter preferences, as well as exploring whether the very circuit is necessary for performing the function well.</div></td></tr>
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</table>Lgdeerhttp://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&diff=181760&oldid=prevEvamonlight: /* References */2010-10-27T13:00:59Z<p><span class="autocomment">References</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Any problem, please contact with <b>Zhenzhen Yin</b><i> evamail.pku AT gmail.com </i>Or <b>Yuheng Lu</b> <i>lgdeer AT gmail.com</i></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Any problem, please contact with <b>Zhenzhen Yin</b><i> evamail.pku AT gmail.com </i>Or <b>Yuheng Lu</b> <i>lgdeer AT gmail.com</i></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>For more clear pictures, please click on it.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><b></ins>For more clear pictures, please click on it.<ins class="diffchange diffchange-inline"></b></ins></div></td></tr>
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</table>Evamonlighthttp://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&diff=181736&oldid=prevEvamonlight: /* References */2010-10-27T12:59:56Z<p><span class="autocomment">References</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Any problem, please contact with <b>Zhenzhen Yin</b><i> evamail.pku AT gmail.com </i>Or <b>Yuheng Lu</b> <i>lgdeer AT gmail.com</i></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Any problem, please contact with <b>Zhenzhen Yin</b><i> evamail.pku AT gmail.com </i>Or <b>Yuheng Lu</b> <i>lgdeer AT gmail.com</i></div></td></tr>
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</table>Evamonlighthttp://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&diff=179882&oldid=prevEvamonlight: /* Introduction */2010-10-27T11:33:09Z<p><span class="autocomment">Introduction</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Introduction=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Introduction=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The biological systems are full of noises, and the response of bioreporters represents a Hill Function. Noises will be significantly amplified and the output detected will be invalid at the ends of dose response curve.(Figure 1(a)) Therefore, The detection is limited at a narrow range. In order to solve the problem, we seek to transform the Hill Function curve to a straight line. As Figure 1(a) shows, the noise is reducted, and the sensitivity and detectable-range-characteristic of biosensors will be significantly improved. <br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The biological systems are full of noises, and the response of bioreporters represents a Hill Function. Noises will be significantly amplified and the output detected will be invalid at the ends of dose response curve.(Figure 1(a)) Therefore, The detection is limited at a narrow range. In order to solve the problem, we seek to transform the Hill Function curve to a straight line. As Figure 1(a) shows, the noise is reducted, and the sensitivity and detectable-range-characteristic of biosensors will be significantly improved. <br><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><html></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Aimed at finding a genetic circuit that can perform the transformation, a simple and universal one for practice convenience, we adopted the process of <ins class="diffchange diffchange-inline">[[Team:Peking/Notebook/Vocabulary#</ins>Reverse <ins class="diffchange diffchange-inline">engineering|Reverse engineering]] </ins>which in our work means to enumerate all possible networks and analyzed whether they function well, thus getting the right topology. In details, we first express the target functionalities in quantitative characters and set numerical standards according to our expectations, next define the network for simplest circuit search and derive equations precisely describing it, then calculate the characters using the equations and compare them with standards, then further analyze the comparison results and find the simplest functional network. Finally, to fully understand it and provide enough information for application, we analyze the mechanism and the parameter preferences, as well as exploring whether the very circuit is necessary for performing the function well.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Aimed at finding a genetic circuit that can perform the transformation, a simple and universal one for practice convenience, we adopted the process of Reverse <del class="diffchange diffchange-inline">Engineering </del>which in our work means to enumerate all possible networks and analyzed whether they function well, thus getting the right topology. In details, we first express the target functionalities in quantitative characters and set numerical standards according to our expectations, next define the network for simplest circuit search and derive equations precisely describing it, then calculate the characters using the equations and compare them with standards, then further analyze the comparison results and find the simplest functional network. Finally, to fully understand it and provide enough information for application, we analyze the mechanism and the parameter preferences, as well as exploring whether the very circuit is necessary for performing the function well.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Here we name our target functionality as Input-Output Alignment(IOA). In order to define IOA precisely for need of calculation, we considered most important characters of IOA and adopted Pearson Correlation Coefficient r to represent Input-Output Linear Relationship in the overall search work ( when r>0.99 we consider the network topology having the IOA function ), and also, regulated two levels for the initial and ultimate output concentration for the second character – the output range in further search work.(Figure 1(b))</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Here we name our target functionality as Input-Output Alignment(IOA). In order to define IOA precisely for need of calculation, we considered most important characters of IOA and adopted Pearson Correlation Coefficient r to represent Input-Output Linear Relationship in the overall search work ( when r>0.99 we consider the network topology having the IOA function ), and also, regulated two levels for the initial and ultimate output concentration for the second character – the output range in further search work.(Figure 1(b))</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Intro2.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Intro2.png|center|600px]]</div></td></tr>
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</table>Evamonlighthttp://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&diff=179829&oldid=prevEvamonlight: /* Introduction */2010-10-27T11:30:13Z<p><span class="autocomment">Introduction</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Introduction=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Introduction=</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The biological systems are full of noises, and the response of bioreporters represents a Hill Function. Noises will be significantly amplified and the output detected will be invalid at the ends of dose response curve.(Figure 1(a)) Therefore, The detection is limited at a narrow range. In order to solve the problem, we seek to transform the Hill Function curve to a straight line. As Figure 1(a) shows, the noise is reducted, and the sensitivity and detectable-range-characteristic of biosensors will be significantly improved. <br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The biological systems are full of noises, and the response of bioreporters represents a Hill Function. Noises will be significantly amplified and the output detected will be invalid at the ends of dose response curve.(Figure 1(a)) Therefore, The detection is limited at a narrow range. In order to solve the problem, we seek to transform the Hill Function curve to a straight line. As Figure 1(a) shows, the noise is reducted, and the sensitivity and detectable-range-characteristic of biosensors will be significantly improved. <ins class="diffchange diffchange-inline"><br></ins><br></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Aimed at finding a genetic circuit that can perform the transformation, a simple and universal one for practice convenience, we adopted the process of Reverse Engineering which in our work means to enumerate all possible networks and analyzed whether they function well, thus getting the right topology. In details, we first express the target functionalities in quantitative characters and set numerical standards according to our expectations, next define the network for simplest circuit search and derive equations precisely describing it, then calculate the characters using the equations and compare them with standards, then further analyze the comparison results and find the simplest functional network. Finally, to fully understand it and provide enough information for application, we analyze the mechanism and the parameter preferences, as well as exploring whether the very circuit is necessary for performing the function well.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Aimed at finding a genetic circuit that can perform the transformation, a simple and universal one for practice convenience, we adopted the process of Reverse Engineering which in our work means to enumerate all possible networks and analyzed whether they function well, thus getting the right topology. In details, we first express the target functionalities in quantitative characters and set numerical standards according to our expectations, next define the network for simplest circuit search and derive equations precisely describing it, then calculate the characters using the equations and compare them with standards, then further analyze the comparison results and find the simplest functional network. Finally, to fully understand it and provide enough information for application, we analyze the mechanism and the parameter preferences, as well as exploring whether the very circuit is necessary for performing the function well.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Here we name our target functionality as Input-Output Alignment(IOA). In order to define IOA precisely for need of calculation, we considered most important characters of IOA and adopted Pearson Correlation Coefficient r to represent Input-Output Linear Relationship in the overall search work ( when r>0.99 we consider the network topology having the IOA function ), and also, regulated two levels for the initial and ultimate output concentration for the second character – the output range in further search work.(Figure 1(b))</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Here we name our target functionality as Input-Output Alignment(IOA). In order to define IOA precisely for need of calculation, we considered most important characters of IOA and adopted Pearson Correlation Coefficient r to represent Input-Output Linear Relationship in the overall search work ( when r>0.99 we consider the network topology having the IOA function ), and also, regulated two levels for the initial and ultimate output concentration for the second character – the output range in further search work.(Figure 1(b))</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Intro2.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Intro2.png|center|600px]]</div></td></tr>
</table>Evamonlighthttp://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&diff=179799&oldid=prevEvamonlight: /* References */2010-10-27T11:28:46Z<p><span class="autocomment">References</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Any problem, please contact with <b>Zhenzhen Yin</b><i> <del class="diffchange diffchange-inline"><</del>evamail.pku AT gmail.com<del class="diffchange diffchange-inline">> </del></i><del class="diffchange diffchange-inline">or </del><b>Yuheng Lu</b> <i><del class="diffchange diffchange-inline"><</del>lgdeer AT gmail.com<del class="diffchange diffchange-inline">></del></i></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Any problem, please contact with <b>Zhenzhen Yin</b><i> evamail.pku AT gmail.com </i><ins class="diffchange diffchange-inline">Or </ins><b>Yuheng Lu</b> <i>lgdeer AT gmail.com</i></div></td></tr>
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</table>Evamonlighthttp://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&diff=179784&oldid=prevEvamonlight: /* References */2010-10-27T11:27:57Z<p><span class="autocomment">References</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Any problem, please contact with <b>Zhenzhen Yin</b><i> evamail.pku AT gmail.com </i>or <b>Yuheng Lu</b> <i>lgdeer AT gmail.com</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Any problem, please contact with <b>Zhenzhen Yin</b><i> <ins class="diffchange diffchange-inline"><</ins>evamail.pku AT gmail.com<ins class="diffchange diffchange-inline">> </ins></i>or <b>Yuheng Lu</b> <i><ins class="diffchange diffchange-inline"><</ins>lgdeer AT gmail.com<ins class="diffchange diffchange-inline">></i></ins></div></td></tr>
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</table>Evamonlighthttp://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&diff=179761&oldid=prevEvamonlight: /* References */2010-10-27T11:27:00Z<p><span class="autocomment">References</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Any problem, please contact with Zhenzhen Yin<i> evamail.pku AT gmail.com </i>or Yuheng Lu <i>lgdeer AT gmail.com</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Any problem, please contact with <ins class="diffchange diffchange-inline"><b></ins>Zhenzhen Yin<ins class="diffchange diffchange-inline"></b></ins><i> evamail.pku AT gmail.com </i>or <ins class="diffchange diffchange-inline"><b></ins>Yuheng Lu<ins class="diffchange diffchange-inline"></b> </ins><i>lgdeer AT gmail.com</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></html></div></td></tr>
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</table>Evamonlighthttp://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&diff=179743&oldid=prevEvamonlight: /* References */2010-10-27T11:26:06Z<p><span class="autocomment">References</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a href="https://static.igem.org/mediawiki/2010/b/bc/Wiki_semilog.pdf"><font color=000000><img src="https://static.igem.org/mediawiki/2010/9/91/PKU_Adobe_Reader_Logo.jpg" width=20><b><i>PART TWO</i></b></font></a></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a href="https://static.igem.org/mediawiki/2010/b/bc/Wiki_semilog.pdf"><font color=000000><img src="https://static.igem.org/mediawiki/2010/9/91/PKU_Adobe_Reader_Logo.jpg" width=20><b><i>PART TWO</i></b></font></a></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><br></ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Any problem, please contact with Zhenzhen Yin<i> evamail.pku AT gmail.com </i>or Yuheng Lu <i>lgdeer AT gmail.com</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></html></div></td></tr>
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</table>Evamonlighthttp://2010.igem.org/wiki/index.php?title=Team:Peking/Modeling&diff=179697&oldid=prevEvamonlight: /* References */2010-10-27T11:22:55Z<p><span class="autocomment">References</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><b><del class="diffchange diffchange-inline">download </del>the model part materials</b></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><b><ins class="diffchange diffchange-inline">Download </ins>the model part materials</b></div></td></tr>
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