http://2009.igem.org/wiki/index.php?title=Team:Newcastle/PopulationDynamics&feed=atom&action=historyTeam:Newcastle/PopulationDynamics - Revision history2024-03-28T19:11:31ZRevision history for this page on the wikiMediaWiki 1.16.5http://2009.igem.org/wiki/index.php?title=Team:Newcastle/PopulationDynamics&diff=166942&oldid=prevTubularWorld: /* Introduction */2009-10-22T02:58:11Z<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> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[Image:Newcastle 3d max 5.png|128px|right]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The fact that in our project we are removing members of the bacterial population, making them sporulate, but not germinate again, will clearly effect the population dynamics of the growth of B. subtilis in a competitive environment such as the soil</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The fact that in our project we are removing members of the bacterial population, making them sporulate, but not germinate again, will clearly effect the population dynamics of the growth of B. subtilis in a competitive environment such as the soil</div></td></tr>
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</table>TubularWorldhttp://2009.igem.org/wiki/index.php?title=Team:Newcastle/PopulationDynamics&diff=162003&oldid=prevNaw3: /* Introduction */2009-10-22T00:41:34Z<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><del class="diffchange diffchange-inline">Due to </del>our project <del class="diffchange diffchange-inline">being based around taking a section </del>of <del class="diffchange diffchange-inline">our </del>bacterial population, <del class="diffchange diffchange-inline">and </del>making them sporulate, but not germinate again, <del class="diffchange diffchange-inline">we need </del>to make sure that we do not kill off our entire population. Thus we <del class="diffchange diffchange-inline">need </del>to be able to tune our system, so that we can have a large enough percentage of metal sequestering spores to make a positive environmental impact, but also a small enough percentage, so that the population will continue to live and grow.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">The fact that in </ins>our project <ins class="diffchange diffchange-inline">we are removing members </ins>of <ins class="diffchange diffchange-inline">the </ins>bacterial population, making them sporulate, but not germinate again, <ins class="diffchange diffchange-inline">will clearly effect the population dynamics of the growth of B. subtilis in a competitive environment such as the soil</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">We needed </ins>to make sure that we do not kill off our entire population. </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Thus we <ins class="diffchange diffchange-inline">required a method </ins>to be able to tune our system, so that we can have a large enough percentage of metal sequestering spores to make a positive environmental impact, but also a small enough percentage, so that the population will continue to live and grow<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">To achieve his aim, we needed to tinker with the delicate balance that ''Bacillus'' normal maintains between its differentiation states of spores and vegetative cells</ins>.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Novelty in this sub-project ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Novelty in this sub-project ==</div></td></tr>
</table>Naw3http://2009.igem.org/wiki/index.php?title=Team:Newcastle/PopulationDynamics&diff=161065&oldid=prevTubularWorld at 00:11, 22 October 20092009-10-22T00:11:21Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Modelling ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Modelling ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: ''See [[Team:Newcastle/Modeling/Population|Population Modelling]]''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: ''See [[Team:Newcastle/Modeling/Population|Population Modelling]]''</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This section of the project is a model, which describes a high level working of our complete system. It also includes detail from other models, as it uses these in its <del class="diffchange diffchange-inline">descision </del>making processes. The model <del class="diffchange diffchange-inline">is being </del>developed in the Java programming language.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This section of the project is a model <ins class="diffchange diffchange-inline">simulation</ins>, which describes a high level working of our complete system. It also includes detail from other models, as it uses these in its <ins class="diffchange diffchange-inline">decision </ins>making processes. The model <ins class="diffchange diffchange-inline">has been </ins>developed in the Java programming language<ins class="diffchange diffchange-inline">, but also uses other technologies including running CellML models</ins>.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Other Presentations and Diagrams ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Other Presentations and Diagrams ==</div></td></tr>
</table>TubularWorldhttp://2009.igem.org/wiki/index.php?title=Team:Newcastle/PopulationDynamics&diff=145523&oldid=prevTubularWorld at 14:36, 21 October 20092009-10-21T14:36:52Z<p></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>Due to our project being based around taking a section of our bacterial population, and making them sporulate, but not germinate again<del class="diffchange diffchange-inline">. Thus </del>we need to make sure that we do not kill off our entire population. <del class="diffchange diffchange-inline">We </del>need to be able to tune our system, so that we can have a large enough percentage of metal sequestering spores to make a positive environmental impact, but also a small enough percentage, so that the population will continue to live and grow.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Due to our project being based around taking a section of our bacterial population, and making them sporulate, but not germinate again<ins class="diffchange diffchange-inline">, </ins>we need to make sure that we do not kill off our entire population. <ins class="diffchange diffchange-inline">Thus we </ins>need to be able to tune our system, so that we can have a large enough percentage of metal sequestering spores to make a positive environmental impact, but also a small enough percentage, so that the population will continue to live and grow.</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>== Novelty in this sub-project ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Novelty in this sub-project ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The novel part of this sub-project is to model the dynamics of a bacterial population, on the cellular level, as well as integrating this agent based model with biochemical models. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The novel part of this sub-project is to model the dynamics of a bacterial population, on the cellular level, as well as integrating this agent based model with biochemical models<ins class="diffchange diffchange-inline">. Furthermore our simulation is able to run on distributed systems, making use of a large number of computers at once</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>== Modelling ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Modelling ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>: ''See [[Team:Newcastle/Modeling/Population]]''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>: ''See [[Team:Newcastle/Modeling/Population<ins class="diffchange diffchange-inline">|Population Modelling</ins>]]''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This section of the project is a model, which describes a high level working of our complete system. It also includes detail from other models, as it uses these in its descision making processes. The model is being developed in the Java programming language.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This section of the project is a model, which describes a high level working of our complete system. It also includes detail from other models, as it uses these in its descision making processes. The model is being developed in the Java programming language.</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>
</table>TubularWorldhttp://2009.igem.org/wiki/index.php?title=Team:Newcastle/PopulationDynamics&diff=145469&oldid=prevTubularWorld at 14:34, 21 October 20092009-10-21T14:34:16Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Newcastle Population Life Cycle 1.png|center|512px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Newcastle Population Life Cycle 1.png|center|512px]]</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>Whereas our modified life cycle would have an additional state, where some spores cannot germinate:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Whereas our modified life cycle would have an additional state, where some spores cannot germinate<ins class="diffchange diffchange-inline">. Notice that cells can enter the Metal Spore stage, but not exit it</ins>:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Newcastle Population Life Cycle 2.png|center|512px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Newcastle Population Life Cycle 2.png|center|512px]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Footer}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Footer}}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Right}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Right}}</div></td></tr>
</table>TubularWorldhttp://2009.igem.org/wiki/index.php?title=Team:Newcastle/PopulationDynamics&diff=142418&oldid=prevTubularWorld at 11:35, 21 October 20092009-10-21T11:35:19Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Other Presentations and Diagrams ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Other Presentations and Diagrams ==</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;">For the population simulation we will be looking at a simplified model of a bacteria's life cycle.</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;"></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;">A simplified normal life cycle may be:</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;">[[Image:Newcastle Population Life Cycle 1.png|center|512px]]</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;"></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;">Whereas our modified life cycle would have an additional state, where some spores cannot germinate:</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;">[[Image:Newcastle Population Life Cycle 2.png|center|512px]]</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Footer}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Footer}}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Right}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Right}}</div></td></tr>
</table>TubularWorldhttp://2009.igem.org/wiki/index.php?title=Team:Newcastle/PopulationDynamics&diff=54556&oldid=prevTubularWorld at 09:22, 27 August 20092009-08-27T09:22:13Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Left}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Left}}</div></td></tr>
<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>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>=Population Dynamics=</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>= Population Dynamics =</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>==Introduction==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>== Introduction ==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Due to our project being based around taking a section of our bacterial population, and making them sporulate, but not germinate again. Thus we need to make sure that we do not kill off our entire population. We need to be able to tune our system, so that we can have a large enough percentage of metal sequestering spores to make a positive environmental impact, but also a small enough percentage, so that the population will continue to live and grow.</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: #ffa; color:black; font-size: smaller;"><div>==Novelty in this sub-project==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>== Novelty in this sub-project ==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">The novel part of this sub-project is to model the dynamics of a bacterial population, on the cellular level, as well as integrating this agent based model with biochemical models. </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: #ffa; color:black; font-size: smaller;"><div>==Modelling==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>== Modelling ==</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">: ''See [[Team:Newcastle/Modeling/Population]]''</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 class="diffchange diffchange-inline">This section of the project is a model, which describes a high level working of our complete system. It also includes detail from other models, as it uses these in its descision making processes. The model is being developed in the Java programming language.</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: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">==BioBrick constructs==</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>== Other Presentations and Diagrams ==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </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: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">==Lab Work Strategies==</del></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: #ffa; color:black; font-size: smaller;"><div> </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: #ffa; color:black; font-size: smaller;"><div>==Other Presentations and Diagrams==</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>{{:Team:Newcastle/Right}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{:Team:Newcastle/Right}}</div></td></tr>
</table>TubularWorldhttp://2009.igem.org/wiki/index.php?title=Team:Newcastle/PopulationDynamics&diff=45947&oldid=prevBabyneurone: New page: {{:Team:Newcastle/CSS}} {{:Team:Newcastle/Header}} {{:Team:Newcastle/Left}} __NOTOC__ =Population Dynamics= ==Introduction== ==Novelty in this sub-project== ==Modelling== ==BioBrick co...2009-08-13T22:29:02Z<p>New page: {{:Team:Newcastle/CSS}} {{:Team:Newcastle/Header}} {{:Team:Newcastle/Left}} __NOTOC__ =Population Dynamics= ==Introduction== ==Novelty in this sub-project== ==Modelling== ==BioBrick co...</p>
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=Population Dynamics=<br />
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==Introduction==<br />
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==Novelty in this sub-project==<br />
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==Modelling==<br />
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==BioBrick constructs==<br />
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==Lab Work Strategies==<br />
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