IGEM:Imperial/2010/Objectives
Objectives
Week 6
Day | Monday | Tuesday | Wednesday | Thursday | Friday |
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Date | 09 | 10 | 11 | 12 | 13 |
Objective | Find constants | Find protein production constants and TEV reaction rate constants | |||
Completion | We didn't manage to complete the task | The orders of magnitude established - ready to run simulations |
Week 7
<html> <table width="1000px" border="0">
<tr> <td style="background-color:#FFFF66"> <b>Day</b> </td> <td style="background-color:#FFFF99;"><b>Monday</b> </td> <td style="background-color:#FFFF99;"><b>Tuesday</b> </td> <td style="background-color:#FFFF99;"><b>Wednesday</b> </td> <td style="background-color:#FFFF99;"><b>Thursday</b> </td> <td style="background-color:#FFFF99;"><b>Friday</b> </td> </tr> <tr> <td style="background-color:#FFCC66;width:100px;text-align:top;"><b>Objectives</b> </td> <td style="background-color:#eeeeee;height:200px;width:300px;text-align:top;"> <ul>
<li>Implementing the constant ranges in the output model.</li> <li>Comparing the results between the models.</li </ul>
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<td style="background-color:#eeeeee;height:200px;width:300px;text-align:top;"> <ul> <li>Start modelling the protein display signalling to find the concentrations.</li> <li>Explain the oscillations that are occuring in the output amplification model</li> </ul>
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<td style="background-color:#eeeeee;height:200px;width:300px;text-align:top;"> <ul> <li>Research stiff differential equations.</li> <li>Research on receptor (especially MAP kinase).</li> <li>Finalise results for amplification model.</li> <li>Prepare presentation.</li> </ul>
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<td style="background-color:#eeeeee;height:200px;width:300px;text-align:top;"> <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> </ul>
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<td style="background-color:#eeeeee;height:200px;width:300px;text-align:top;"> <ul> <li>Discuss the experiments for amplification module further.</li> <li>Start on modelling the protein display on cell surface.</li> </ul>
</td> </tr> <tr> <td style="background-color:#FFCC66;width:100px;text-align:top;"><b>Completion</b> </td> <td style="background-color:#eeeeee;height:200px;width:300px;text-align:top;">
<ul> <li>The task is accomplished. However, unexplained oscillations are observed for some specific values.</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:300px;text-align:top;"> <ul> <li>We got rid of the oscillations in our model (by using ode15s instead of ode45).</li> </ul>
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<td style="background-color:#eeeeee;height:200px;width:300px;text-align:top;"> <ul> <li>Presentation ready.</li> <li>Reading on stiff equations done.</li> </ul>
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<td style="background-color:#eeeeee;height:200px;width:300px;text-align:top;"> <ul> <li>Key sensitive parameters determined.</li> <li>Experiments initially discussed with Chris.</li> </ul>
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<td style="background-color:#eeeeee;height:200px;width:300px;text-align:top;"> <ul> <li>Further consult on experiments for determining parameters needed for modelling with James and Wolf.</li> <li>Initial thought for a protein display model implemented in MatLab.</li> </ul>
</td> </tr>
</table> </html>
Day | Monday | Tuesday | Wednesday | Thursday | Friday |
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Date | 16 | 17 | 18 | 19 | 20 |
Objective | Implementing the constant ranges in the output model. Comparing the results between the models. |
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Completion | The task is accomplished. However, unexplained oscillations are observed for some specific values |
We got rid of the oscillations in our model (by using ode15s instead of ode45). |
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Week 8
Day | Monday | Tuesday | Wednesday | Thursday | Friday |
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Date | 23 | 24 | 25 | 26 | 27 |
Objective | Test the protein display model and find to what kind of values it's sensitive to |
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Completion | 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. |
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Week 9
Day | Monday | Tuesday | Wednesday | Thursday | Friday |
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Date | 30 | 31 | 01 | 02 | 03 |
Objective | Bank holiday |
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Completion |
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Week 10
Day | Monday | Tuesday | Wednesday | Thursday | Friday |
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Date | 06 | 07 | 08 | 09 | 10 |
Objective | |||||
Completion |