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ETHZ/Engineering - Revision history
2024-03-28T13:27:46Z
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LiNan at 23:37, 24 October 2007
2007-10-24T23:37:03Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | Biology Pespective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Engineering | Engineering Perspective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | Biology Pespective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Engineering | Engineering Perspective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br></div></td></tr>
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LiNan
http://2007.igem.org/wiki/index.php?title=ETHZ/Engineering&diff=27144&oldid=prev
Kdikaiou at 13:06, 18 October 2007
2007-10-18T13:06:10Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>__NOTOC__</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>__NOTOC__</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Model | System Modeling]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | System Implementation]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/<del class="diffchange diffchange-inline">Internal </del>| Lab Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Model | System Modeling]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | System Implementation]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/<ins class="diffchange diffchange-inline">Biology/Lab</ins>| Lab Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br></div></td></tr>
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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>
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Kdikaiou
http://2007.igem.org/wiki/index.php?title=ETHZ/Engineering&diff=26419&oldid=prev
Cbergeles at 19:59, 16 October 2007
2007-10-16T19:59:22Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | Biology Pespective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Engineering | Engineering Perspective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | Biology Pespective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Engineering | Engineering Perspective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br></div></td></tr>
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Cbergeles
http://2007.igem.org/wiki/index.php?title=ETHZ/Engineering&diff=26405&oldid=prev
Cbergeles at 19:55, 16 October 2007
2007-10-16T19:55:57Z
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Model | System Modeling]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | System Implementation]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Lab Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Model | System Modeling]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | System Implementation]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Lab Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center<ins class="diffchange diffchange-inline">><br</ins>></div></td></tr>
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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>
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Cbergeles
http://2007.igem.org/wiki/index.php?title=ETHZ/Engineering&diff=26404&oldid=prev
Cbergeles at 19:55, 16 October 2007
2007-10-16T19:55:46Z
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><center<del class="diffchange diffchange-inline">><font size = '+1'><b> .:: educatETH <i>E.coli</i> - Engineering Perspective ::. </b></font></center><br></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><center><ins class="diffchange diffchange-inline">[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; </ins>[[ETHZ/Model | <ins class="diffchange diffchange-inline">System Modeling</ins>]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/<ins class="diffchange diffchange-inline">Biology </ins>| <ins class="diffchange diffchange-inline">System Implementation</ins>]] <ins class="diffchange diffchange-inline">&nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ</ins>/<ins class="diffchange diffchange-inline">Internal | Lab Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</ins></center></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><center><font size = '-1'</del>>[[ETHZ/Model | <del class="diffchange diffchange-inline">Model</del>]]&nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/<del class="diffchange diffchange-inline">Parameters </del>| <del class="diffchange diffchange-inline"> Parameters</del>]]<del class="diffchange diffchange-inline"><</del>/<del class="diffchange diffchange-inline">font></del></center></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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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>
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Cbergeles
http://2007.igem.org/wiki/index.php?title=ETHZ/Engineering&diff=26351&oldid=prev
Brutsche: /* .:: System Model ::. */
2007-10-16T16:06:47Z
<p><span class="autocomment">.:: System Model ::.</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| l<sup>hi</sup></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| l<sup>hi</sup></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| 25</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| 25</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| <del class="diffchange diffchange-inline">high</del>-copy plasmid number</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| <ins class="diffchange diffchange-inline">mid</ins>-copy plasmid number</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Estimate</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Estimate</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
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Brutsche
http://2007.igem.org/wiki/index.php?title=ETHZ/Engineering&diff=26246&oldid=prev
LiNan at 13:00, 16 October 2007
2007-10-16T13:00:23Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The subsystem of the constitutively produced proteins serves as a regulatory system, and can be modeled with the following three decoupled partial differential equations (see Fig. 1):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The subsystem of the constitutively produced proteins serves as a regulatory system, and can be modeled with the following three decoupled partial differential equations (see Fig. 1):</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:constitutive_part.png|center|thumb|<del class="diffchange diffchange-inline">Subsystem </del>1: Constitutively produced proteins <del class="diffchange diffchange-inline">(Fig. 1)</del>|340px]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:constitutive_part.png|center|thumb|<ins class="diffchange diffchange-inline">'''Fig.</ins>1: <ins class="diffchange diffchange-inline">'''Subsystem 1-</ins>Constitutively produced proteins|340px]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The second subsystem is the main part of our model. It stores the information concerning the learned information for the chemical of interest, and drives the production of the appropriate reporter during the recognition phase. It is actually a toggle switch that reaches its steady state depending on the chemical that it has been previously exposed to (see Fig. 2):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The second subsystem is the main part of our model. It stores the information concerning the learned information for the chemical of interest, and drives the production of the appropriate reporter during the recognition phase. It is actually a toggle switch that reaches its steady state depending on the chemical that it has been previously exposed to (see Fig. 2):</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:toggle_part_b.png|center|thumb|Subsystem 2<del class="diffchange diffchange-inline">: </del>Basic learning subsystem (toggle<del class="diffchange diffchange-inline">) (Fig. 2</del>)|900px]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:toggle_part_b.png|center|thumb|<ins class="diffchange diffchange-inline">'''Fig.2: '''</ins>Subsystem 2<ins class="diffchange diffchange-inline">-</ins>Basic learning subsystem (toggle)|900px]]</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>The third subsystem reports the state that our system is, during the different phases of learning and recognition. During the learning phase, this subsystem reports which chemical the cells are exposed to, and during the recognition phase, it reports if the cells recognize the chemicals that they are currently exposed to (see Fig. 3):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The third subsystem reports the state that our system is, during the different phases of learning and recognition. During the learning phase, this subsystem reports which chemical the cells are exposed to, and during the recognition phase, it reports if the cells recognize the chemicals that they are currently exposed to (see Fig. 3):</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:reporting_part_b.png|center|thumb|<del class="diffchange diffchange-inline">Subsystem </del>3: Reporting subsystem <del class="diffchange diffchange-inline">(Fig. 3)</del>|900px]] </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:reporting_part_b.png|center|thumb|<ins class="diffchange diffchange-inline">'''Fig.</ins>3: <ins class="diffchange diffchange-inline">'''Subsystem 3-</ins>Reporting subsystem |900px]] </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>Note that the three constitutively produced proteins LacI, TetR and LuxR exist in two different forms; as free proteins and in complexes they build with IPTG, aTc and AHL, respectively. We need to model this complex-forming procedure, with another set of differential equations (Fig. 4):</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Note that the three constitutively produced proteins LacI, TetR and LuxR exist in two different forms; as free proteins and in complexes they build with IPTG, aTc and AHL, respectively. We need to model this complex-forming procedure, with another set of differential equations (Fig. 4):</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:allosteric_part.png|center|thumb|<del class="diffchange diffchange-inline">Allosteric regulation (see </del>Fig. 4<del class="diffchange diffchange-inline">)</del>|240px]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:allosteric_part.png|center|thumb|<ins class="diffchange diffchange-inline">'''</ins>Fig.4<ins class="diffchange diffchange-inline">: '''Allosteric regulation</ins>|240px]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to have meaningful results from our simulations, we browsed through the literature in order to find appropriate values for our parameters. We reduced our parameter space by joining parameters together, and we gave reasonable estimates, for the values that could not be extracted from available publications. Since this is a hard part that every team has to face, we present the table with the chosen parameters below:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to have meaningful results from our simulations, we browsed through the literature in order to find appropriate values for our parameters. We reduced our parameter space by joining parameters together, and we gave reasonable estimates, for the values that could not be extracted from available publications. Since this is a hard part that every team has to face, we present the table with the chosen parameters below:</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:parameters.png|center|thumb|Parameters of the model <del class="diffchange diffchange-inline">(Fig. 5)</del>|800px]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:parameters.png|center|thumb|<ins class="diffchange diffchange-inline">'''Fig.5: '''</ins>Parameters of the model|800px]]</div></td></tr>
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LiNan
http://2007.igem.org/wiki/index.php?title=ETHZ/Engineering&diff=26241&oldid=prev
LiNan at 12:52, 16 October 2007
2007-10-16T12:52:12Z
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><center><font size = '+1'><b> .:: <del class="diffchange diffchange-inline">EducatETH </del><i>E. coli</i> - Engineering Perspective ::. </b></font></center><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><center><font size = '+1'><b> .:: <ins class="diffchange diffchange-inline">educatETH </ins><i>E.coli</i> - Engineering Perspective ::. </b></font></center><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center><font size = '-1'>[[ETHZ/Model | Model]]&nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Parameters | Parameters]]</font></center></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center><font size = '-1'>[[ETHZ/Model | Model]]&nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Parameters | Parameters]]</font></center></div></td></tr>
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LiNan
http://2007.igem.org/wiki/index.php?title=ETHZ/Engineering&diff=26038&oldid=prev
Kdikaiou at 14:56, 15 October 2007
2007-10-15T14:56:26Z
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><center>[[ETHZ<del class="diffchange diffchange-inline">/Main_page </del>| Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | Biology Pespective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Engineering | Engineering Perspective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | Biology Pespective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Engineering | Engineering Perspective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br></div></td></tr>
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Kdikaiou
http://2007.igem.org/wiki/index.php?title=ETHZ/Engineering&diff=26030&oldid=prev
Kdikaiou at 14:48, 15 October 2007
2007-10-15T14:48:36Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center><font size = '+1'><b> .:: EducatETH <i>E. coli</i> - Engineering Perspective ::. </b></font></center><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center><font size = '+1'><b> .:: EducatETH <i>E. coli</i> - Engineering Perspective ::. </b></font></center><br></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;"><center><font size = '-1'>[[ETHZ/Model | Model]]&nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Parameters | Parameters]]</font></center></ins></div></td></tr>
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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>
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Kdikaiou