Team:Imperial College London/Modelling/Objectives
From 2010.igem.org
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- | + | <ul> | |
+ | <li>Find the partial differential equations that describe our system according to Law of Mass action</li> | ||
+ | <li>Start implementing it into MatLab</li> | ||
+ | </ul> | ||
+ | </td> | ||
<td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"> | <td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"> | ||
<ul> | <ul> | ||
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</td> | </td> | ||
<td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"> | <td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"> | ||
+ | <ul> | ||
+ | <li>Finish implementing the model into MatLab and TinkerCell</li> | ||
+ | </ul> | ||
</td> | </td> | ||
<td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"> | <td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"> | ||
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<td style="background-color:#eeeeee;height:100px;text-align:top;"> | <td style="background-color:#eeeeee;height:100px;text-align:top;"> | ||
+ | <ul> | ||
+ | <li>We got loads of equations for 2-step amplification model so we did not manage to implement all models</li> | ||
+ | </ul> | ||
</td> | </td> | ||
<td style="background-color:#eeeeee;height:100px;text-align:top;"> | <td style="background-color:#eeeeee;height:100px;text-align:top;"> | ||
+ | <ul> | ||
+ | <li>Implementation in TinkerCell proved to be quite intuitive and was done.</li> | ||
+ | </ul> | ||
</td> | </td> | ||
<td style="background-color:#eeeeee;height:100px;text-align:top;"> | <td style="background-color:#eeeeee;height:100px;text-align:top;"> | ||
+ | <ul> | ||
+ | <li>Implementation of codes was completed today.</li> | ||
+ | <li>TinkerCell and MatLab generate similar results.</li> | ||
+ | </ul> | ||
</td> | </td> | ||
<td style="background-color:#eeeeee;height:100px;text-align:top;"> | <td style="background-color:#eeeeee;height:100px;text-align:top;"> | ||
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|} | |} | ||
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- | + | |style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"|Week 7 | |
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- | <html> | + | |- |
- | <table width=" | + | |<html> |
+ | <table width="850px" border="0"> | ||
<tr> | <tr> | ||
<td style="background-color:#FFFF66;text-align:center"> | <td style="background-color:#FFFF66;text-align:center"> | ||
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<td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Objectives</b> | <td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Objectives</b> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Implementing the constant ranges in the output model.</li> | <li>Implementing the constant ranges in the output model.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Start modelling the protein display signalling to find the concentrations.</li> | <li>Start modelling the protein display signalling to find the concentrations.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Research stiff differential equations.</li> | <li>Research stiff differential equations.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>During the meeting it was decided that we should test amplificiation model for its sensitivity to change of parameter values. This is to determine the key parameters to be measured in the lab.</li> | <li>During the meeting it was decided that we should test amplificiation model for its sensitivity to change of parameter values. This is to determine the key parameters to be measured in the lab.</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Discuss the experiments for amplification module further.</li> | <li>Discuss the experiments for amplification module further.</li> | ||
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<td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Completion</b> | <td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Completion</b> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>The task is accomplished. However, unexplained oscillations are observed for some specific values.</li> | <li>The task is accomplished. However, unexplained oscillations are observed for some specific values.</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>We got rid of the oscillations in our model (by using ode15s instead of ode45).</li> | <li>We got rid of the oscillations in our model (by using ode15s instead of ode45).</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Presentation ready.</li> | <li>Presentation ready.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Key sensitive parameters determined.</li> | <li>Key sensitive parameters determined.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Further consult on experiments for determining parameters needed for modelling with James and Wolf.</li> | <li>Further consult on experiments for determining parameters needed for modelling with James and Wolf.</li> | ||
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</table> | </table> | ||
</html> | </html> | ||
+ | |} | ||
- | + | {| style="width:900px;background:#f5f5f5;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20" | |
- | + | |style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"|Week 8 | |
- | + | ||
- | <html> | + | |- |
- | <table width=" | + | |<html> |
+ | <table width="850px" border="0"> | ||
<tr> | <tr> | ||
<td style="background-color:#FFFF66;text-align:center"> | <td style="background-color:#FFFF66;text-align:center"> | ||
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<td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Objectives</b> | <td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Objectives</b> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Test the protein display model and find to what kind of values it's sensitive to.</li> | <li>Test the protein display model and find to what kind of values it's sensitive to.</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Define the control volume around the bacterial cell.</li> | <li>Define the control volume around the bacterial cell.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>We realised that it would be worth adding the last step (colour production by dioxygenase) into our amplfication models.</li> | <li>We realised that it would be worth adding the last step (colour production by dioxygenase) into our amplfication models.</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>We need to finalise testing and formulation of certain assumptions regarding the amplfication (cell death in particular).</li> | <li>We need to finalise testing and formulation of certain assumptions regarding the amplfication (cell death in particular).</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Keep exploring the prospective solutions to our system going unstable.</li> | <li>Keep exploring the prospective solutions to our system going unstable.</li> | ||
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<td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Completion</b> | <td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Completion</b> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height | + | <td style="background-color:#eeeeee;height:200px;text-align:top;"> |
<ul> | <ul> | ||
<li>We couldn't reach the testing as the first model "Display 1" was simulating reactions as if the were taking place inside the bacterial cell while in reality the take place outside. Then we hit an issue of defining the size of volume around the cell. We didn't manage to resolve that problem today.</li> | <li>We couldn't reach the testing as the first model "Display 1" was simulating reactions as if the were taking place inside the bacterial cell while in reality the take place outside. Then we hit an issue of defining the size of volume around the cell. We didn't manage to resolve that problem today.</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height | + | <td style="background-color:#eeeeee;height:200px;text-align:top;"> |
<ul> | <ul> | ||
<li>Control volume defined.</li> | <li>Control volume defined.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height | + | <td style="background-color:#eeeeee;height:200px;text-align:top;"> |
<ul> | <ul> | ||
<li>The colour production almost complete, however complications were encountered regarding the cell death (colour compound slowly kills cells).</li> | <li>The colour production almost complete, however complications were encountered regarding the cell death (colour compound slowly kills cells).</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height | + | <td style="background-color:#eeeeee;height:200px;text-align:top;"> |
<ul> | <ul> | ||
<li>Basically we're stuck: scaling didn't help neither did trying idfferent solvers.</li> | <li>Basically we're stuck: scaling didn't help neither did trying idfferent solvers.</li> | ||
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</table> | </table> | ||
</html> | </html> | ||
+ | |} | ||
- | + | {| style="width:900px;background:#f5f5f5;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20" | |
- | + | |style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"|Week 9 | |
- | + | ||
- | <html> | + | |- |
- | <table width=" | + | |<html> |
+ | <table width="850px" border="0"> | ||
<tr> | <tr> | ||
<td style="background-color:#FFFF66;text-align:center"> | <td style="background-color:#FFFF66;text-align:center"> | ||
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<td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Objectives</b> | <td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Objectives</b> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height: | + | <td style="background-color:#eeeeee;height:150px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Bank Holiday</li> | <li>Bank Holiday</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Compare Tinker Cell results against MatLab simulations (Amplficiation model).</li> | <li>Compare Tinker Cell results against MatLab simulations (Amplficiation model).</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Discuss the protein display false positive.</li> | <li>Discuss the protein display false positive.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Update Modelling section of the Wiki.</li> | <li>Update Modelling section of the Wiki.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:200px;width: | + | <td style="background-color:#eeeeee;height:200px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Keep modifying wiki.</li> | <li>Keep modifying wiki.</li> | ||
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<td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Completion</b> | <td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Completion</b> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height | + | <td style="background-color:#eeeeee;height:200px;text-align:top;"> |
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height | + | <td style="background-color:#eeeeee;height:200px;text-align:top;"> |
<ul> | <ul> | ||
<li>Tinkercell is not very good at dealing with very high or low values.</li> | <li>Tinkercell is not very good at dealing with very high or low values.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height | + | <td style="background-color:#eeeeee;height:200px;text-align:top;"> |
<ul> | <ul> | ||
<li>Modelling of false positive in display protein is postponed as more research need to be done on the affinities etc.</li> | <li>Modelling of false positive in display protein is postponed as more research need to be done on the affinities etc.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height | + | <td style="background-color:#eeeeee;height:200px;text-align:top;"> |
<ul> | <ul> | ||
<li>Restructuring modelling wiki is now on!</li> | <li>Restructuring modelling wiki is now on!</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height | + | <td style="background-color:#eeeeee;height:200px;text-align:top;"> |
<ul> | <ul> | ||
<li>Wiki updating will continue next week.</li> | <li>Wiki updating will continue next week.</li> | ||
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</table> | </table> | ||
</html> | </html> | ||
+ | |} | ||
- | + | {| style="width:900px;background:#f5f5f5;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20" | |
- | + | |style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"|Week 10 | |
- | + | ||
- | <html> | + | |- |
- | <table width=" | + | |<html> |
+ | <table width="850px" border="0"> | ||
<tr> | <tr> | ||
<td style="background-color:#FFFF66;text-align:center"> | <td style="background-color:#FFFF66;text-align:center"> | ||
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<td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Objectives</b> | <td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Objectives</b> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:100px;width: | + | <td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Do the referencing of all Modelling Wiki pages.</li> | <li>Do the referencing of all Modelling Wiki pages.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:100px;width: | + | <td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Make new tables for the Objectives section.</li> | <li>Make new tables for the Objectives section.</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:100px;width: | + | <td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Make a jquery accordion list for the first Modelling page.</li> | <li>Make a jquery accordion list for the first Modelling page.</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:100px;width: | + | <td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"> |
<ul> | <ul> | ||
<li>Rewrite pages into html.</li> | <li>Rewrite pages into html.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:100px;width: | + | <td style="background-color:#eeeeee;height:100px;width:150px;text-align:top;"><ul> |
<li>Last day!!!</li> | <li>Last day!!!</li> | ||
<li>Finish rewriting pages into html.</li> | <li>Finish rewriting pages into html.</li> | ||
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<td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Completion</b> | <td style="background-color:#FFCC66;width:100px;text-align:center;"><b>Completion</b> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:100px | + | <td style="background-color:#eeeeee;height:100px;text-align:top;"> |
<ul> | <ul> | ||
<li>Referencing finished.</li> | <li>Referencing finished.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:100px | + | <td style="background-color:#eeeeee;height:100px;text-align:top;"> |
<ul> | <ul> | ||
<li>New tables completed.</li> | <li>New tables completed.</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:100px | + | <td style="background-color:#eeeeee;height:100px;text-align:top;"> |
<ul> | <ul> | ||
<li>List completed.</li> | <li>List completed.</li> | ||
</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:100px | + | <td style="background-color:#eeeeee;height:100px;text-align:top;"> |
<ul> | <ul> | ||
<li>Rewriting into html not yet completed.</li> | <li>Rewriting into html not yet completed.</li> | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | <td style="background-color:#eeeeee;height:100px | + | <td style="background-color:#eeeeee;height:100px;text-align:top;"> |
</td> | </td> | ||
</tr> | </tr> | ||
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</body> | </body> | ||
</html> | </html> | ||
+ | |} |
Revision as of 16:16, 12 October 2010
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