http://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&feed=atom&action=historyTeam:HIT-Harbin/Modeling - Revision history2024-03-28T18:08:21ZRevision history for this page on the wikiMediaWiki 1.16.5http://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&diff=213284&oldid=prevLanqiao at 17:15, 27 September 20132013-09-27T17:15:32Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>PS : Parameters are constants in our model. Variables are what we controlled in one experiment.States are dependent variable changing in one experiment. Observation is our target output</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>PS : Parameters are constants in our model. Variables are what we controlled in one experiment.States are dependent variable changing in one experiment. Observation is our target output</p></div></td></tr>
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</table>Lanqiaohttp://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&diff=201178&oldid=prevSema1688 at 08:20, 27 September 20132013-09-27T08:20:33Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>PS : Parameters are constants in our model. Variables are what we controlled in one experiment.States are dependent variable changing in one experiment. Observation is our target output</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>PS : Parameters are constants in our model. Variables are what we controlled in one experiment.States are dependent variable changing in one experiment. Observation is our target output</p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>[3] Hidde de Jong. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review[J]. Journal of Computational Biology: 2002, 9(1): 67~103</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>[3] Hidde de Jong. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review[J]. Journal of Computational Biology: 2002, 9(1): 67~103</p></div></td></tr>
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</table>Sema1688http://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&diff=199808&oldid=prevSema1688 at 06:59, 27 September 20132013-09-27T06:59:47Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>[3] Hidde de Jong. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review[J]. Journal of Computational Biology: 2002, 9(1): 67~103</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>[3] Hidde de Jong. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review[J]. Journal of Computational Biology: 2002, 9(1): 67~103</p></div></td></tr>
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</table>Sema1688http://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&diff=199791&oldid=prevSema1688 at 06:59, 27 September 20132013-09-27T06:59:11Z<p></p>
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</table>Sema1688http://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&diff=199727&oldid=prevSema1688 at 06:55, 27 September 20132013-09-27T06:55:48Z<p></p>
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</table>Sema1688http://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&diff=180584&oldid=prevSema1688 at 08:47, 26 September 20132013-09-26T08:47:20Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>In the beginning of the project, a mathematical model would be necessary to obtain a clear depict of the system as well as a reasonable expectation of the subsequent experiments. However, to start with, several premises shall be settled in the first step. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>In the beginning of the project, a mathematical model would be necessary to obtain a clear depict of the system as well as a reasonable expectation of the subsequent experiments. However, to start with, several premises shall be settled in the first step. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(1) The transcription follows the Hill equation, while other reactions follow the mass action principle and the saturation kinetics.<p/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(1) The transcription follows the Hill equation, while other reactions follow the mass action principle and the saturation kinetics.<p/></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>(2) Part of the parameter values are obtained according to previous publications, while others are assigned in a reasonable way.<<del class="diffchange diffchange-inline">p</del>/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>(2) Part of the parameter values are obtained according to previous publications, while others are assigned in a reasonable way.</<ins class="diffchange diffchange-inline">p</ins>></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(3) The amount of protein binding to promoter is negligible compared to the total amount of protein.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(3) The amount of protein binding to promoter is negligible compared to the total amount of protein.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>(4) Simulation was done using SBToolbox[4] for matlab and R, a free software environment for statistical computing and graphics<<del class="diffchange diffchange-inline">/</del>p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>(4) Simulation was done using SBToolbox[4] for matlab and R, a free software environment for statistical computing and graphics<p<ins class="diffchange diffchange-inline">/</ins>></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4 class="hashed"><span>The circuit</span></h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4 class="hashed"><span>The circuit</span></h4></div></td></tr>
</table>Sema1688http://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&diff=180564&oldid=prevSema1688 at 08:45, 26 September 20132013-09-26T08:45:41Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(2) Part of the parameter values are obtained according to previous publications, while others are assigned in a reasonable way.<p/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(2) Part of the parameter values are obtained according to previous publications, while others are assigned in a reasonable way.<p/></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(3) The amount of protein binding to promoter is negligible compared to the total amount of protein.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(3) The amount of protein binding to promoter is negligible compared to the total amount of protein.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>(4) Simulation was done using SBToolbox for matlab and R, a free software environment for statistical computing and graphics</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>(4) Simulation was done using SBToolbox<ins class="diffchange diffchange-inline">[4] </ins>for matlab and R, a free software environment for statistical computing and graphics</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4 class="hashed"><span>The circuit</span></h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4 class="hashed"><span>The circuit</span></h4></div></td></tr>
</table>Sema1688http://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&diff=180560&oldid=prevSema1688 at 08:45, 26 September 20132013-09-26T08:45:07Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(2) Part of the parameter values are obtained according to previous publications, while others are assigned in a reasonable way.<p/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(2) Part of the parameter values are obtained according to previous publications, while others are assigned in a reasonable way.<p/></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(3) The amount of protein binding to promoter is negligible compared to the total amount of protein.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(3) The amount of protein binding to promoter is negligible compared to the total amount of protein.</p></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;"><p>(4) Simulation was done using SBToolbox for matlab and R, a free software environment for statistical computing and graphics</p></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4 class="hashed"><span>The circuit</span></h4></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h4 class="hashed"><span>The circuit</span></h4></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>[2] Baojun Wang et al. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology[J]. Nature Communications: 2011, 2</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>[2] Baojun Wang et al. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology[J]. Nature Communications: 2011, 2</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>[3] Hidde de Jong. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review[J]. Journal of Computational Biology: 2002, 9(1): 67~103</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>[3] Hidde de Jong. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review[J]. Journal of Computational Biology: 2002, 9(1): 67~103</p></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;"><p>[4] Schmidt H, Jirstrand M. Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. Bioinformatics2006,22: 514-515</p></ins></div></td></tr>
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</table>Sema1688http://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&diff=180513&oldid=prevSema1688 at 08:40, 26 September 20132013-09-26T08:40:26Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2013/3/37/HIT-Harbin_Project_Table2.png"/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2013/3/37/HIT-Harbin_Project_Table2.png"/></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Here we invent a coefficient <del class="diffchange diffchange-inline"> </del>where b is the concentration range of linear area between output response and IPTG and a the whole range of IPTG concentration. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Here we invent a coefficient <ins class="diffchange diffchange-inline">m(m=b/a) </ins>where b is the concentration range of linear area between output response and IPTG and a the whole range of IPTG concentration. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div align="center"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div align="center"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2013/4/49/HIT-Harbin_Project_SimResult3.png"/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><img src="https://static.igem.org/mediawiki/2013/4/49/HIT-Harbin_Project_SimResult3.png"/></div></td></tr>
</table>Sema1688http://2013.igem.org/wiki/index.php?title=Team:HIT-Harbin/Modeling&diff=162904&oldid=prevLanqiao at 19:02, 24 September 20132013-09-24T19:02:25Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="multi-columns"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> <div class="multi-columns"></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><<del class="diffchange diffchange-inline">h3 </del>class="hashed"><span>Premises</span></<del class="diffchange diffchange-inline">h3</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><<ins class="diffchange diffchange-inline">h4 </ins>class="hashed"><span>Premises</span></<ins class="diffchange diffchange-inline">h4</ins>></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>In the beginning of the project, a mathematical model would be necessary to obtain a clear depict of the system as well as a reasonable expectation of the subsequent experiments. However, to start with, several premises shall be settled in the first step. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>In the beginning of the project, a mathematical model would be necessary to obtain a clear depict of the system as well as a reasonable expectation of the subsequent experiments. However, to start with, several premises shall be settled in the first step. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(1) The transcription follows the Hill equation, while other reactions follow the mass action principle and the saturation kinetics.<p/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(1) The transcription follows the Hill equation, while other reactions follow the mass action principle and the saturation kinetics.<p/></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(3) The amount of protein binding to promoter is negligible compared to the total amount of protein.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>(3) The amount of protein binding to promoter is negligible compared to the total amount of protein.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><<del class="diffchange diffchange-inline">h3 </del>class="hashed"><span>The circuit</span></<del class="diffchange diffchange-inline">h3</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><<ins class="diffchange diffchange-inline">h4 </ins>class="hashed"><span>The circuit</span></<ins class="diffchange diffchange-inline">h4</ins>></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The following picture is the whole design of our circuit.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>The following picture is the whole design of our circuit.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div align="center"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div align="center"></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><<del class="diffchange diffchange-inline">h3 </del>class="hashed"><span>Model of proportional amplifier</span></<del class="diffchange diffchange-inline">h3</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><<ins class="diffchange diffchange-inline">h4 </ins>class="hashed"><span>Model of proportional amplifier</span></<ins class="diffchange diffchange-inline">h4</ins>></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><<del class="diffchange diffchange-inline">h3 </del>class="hashed"><span>Reference</span></<del class="diffchange diffchange-inline">h3</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><<ins class="diffchange diffchange-inline">h4 </ins>class="hashed"><span>Reference</span></<ins class="diffchange diffchange-inline">h4</ins>></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>[1] Baojun Wang. The Design and Construction of a Set of Modular Synthetic BioLogic Devices for Programming Cells. IFMBE 2009</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>[1] Baojun Wang. The Design and Construction of a Set of Modular Synthetic BioLogic Devices for Programming Cells. IFMBE 2009</p></div></td></tr>
</table>Lanqiao