IGEM:Imperial/2010/Objectives: Difference between revisions
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==Week 8== | ==Week 8== | ||
<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:200px;text-align:top;"> | |||
<ul> | |||
<li>Test the protein display model and find to what kind of values it's sensitive to.</li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Define the control volume around the bacterial cell.</li> | |||
<li>Start on testing the model.</li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>We realised that it would be worth adding the last step (colour production by dioxygenase) into our amplfication models.</li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>We need to finalise testing and formulation of certain assumptions regarding the amplfication (cell death in particular).</li> | |||
<li>Consider helping RMIT- Australia in modelling.</li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Keep exploring the prospective solutions to our system going unstable.</li> | |||
<li>Try to implement the last bit of amplification in TinkerCell. Maybe it will deal with it well.</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:200px;text-align:top;"> | |||
<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> | |||
</ul> | |||
</td> | |||
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Control volume defined.</li> | |||
<li>Testing of model done.</li> | |||
<li>Protein model pretty much finalised.</li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>The colour production almost complete, however complications were encountered regarding the cell death (colour compound slowly kills cells).</li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>Basically we're stuck: scaling didn't help neither did trying idfferent solvers.</li> | |||
<li>Meeting with Matthieu gave us some prospective solutions that we can explore.</li> | |||
<li>Alternatively we can have a look at SimBiology or MatCont.</li> | |||
<li>Helping RMIT: their request is for protein engineering simulation - we cannot do that</li> | |||
</ul> | |||
</td> | |||
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> | |||
<ul> | |||
<li>We know how to use the ''splinetool'' in Matlab.</li> | |||
<li>Specifying the time span helps to reduce the simulation time.</li> | |||
<li>Model was implemented in TinkerCell.</li> | |||
<li>Increasing relative or absolute tolerance in Matlab prevents some solutions from going negative. The key point is that we are only interested in the first few minutes of the experiment as the reaction to catechol is really quick.</li> | |||
</ul> | |||
</td> | |||
</tr> | |||
</table> | |||
</html> | |||
{| class="wikitable" style="text-align: center; width: 100%; height: 170px;" border="1" | {| class="wikitable" style="text-align: center; width: 100%; height: 170px;" border="1" | ||
|- | |- | ||
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*helping RMIT - their request is for protein engineering simulation - we cannot do that | *helping RMIT - their request is for protein engineering simulation - we cannot do that | ||
|| | || | ||
*We know how to use the ''splinetool'' in Matlab - it's tool to smoothen noisy graphs allows to manipulate graphs | *We know how to use the ''splinetool'' in Matlab - it's a tool to smoothen noisy graphs allows to manipulate graphs | ||
*We found that specifying time span | *We found that specifying time span instead of specific time array with defined time steps helps to reduce the simulation time. | ||
*Model was implemented in TinkerCell, but we didn't ahve enough time to compare it with Matlab model | *Model was implemented in TinkerCell, but we didn't ahve enough time to compare it with Matlab model | ||
*Increasing relative or absolute tolerance in Matlab prevents some solutions from going negative | *Increasing relative or absolute tolerance in Matlab prevents some solutions from going negative. The key point is that, according to the experiments carried out earlier today, we are interested in the first few minutes of the experiment as the reaction to catechol is really quick. | ||
|} | |} | ||
Revision as of 07:16, 7 September 2010
Objectives
Week 6
<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:100px;width:200px;text-align:top;"> </td>
<td style="background-color:#eeeeee;height:100px;width:200px;text-align:top;">
</td>
<td style="background-color:#eeeeee;height:100px;width:200px;text-align:top;">
</td>
<td style="background-color:#eeeeee;height:100px;width:200px;text-align:top;"> <ul> <li>Find constants.</li> </ul>
</td>
<td style="background-color:#eeeeee;height:100px;width:200px;text-align:top;"> <ul> <li>Find protein production constants and TEV reaction rate constants.</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:100px;width:200px;text-align:top;"> </td>
<td style="background-color:#eeeeee;height:100px;width:200px;text-align:top;">
</td>
<td style="background-color:#eeeeee;height:100px;width:200px;text-align:top;">
</td>
<td style="background-color:#eeeeee;height:100px;width:200px;text-align:top;"> <ul> <li>We didn't manage to complete the task.</li> </ul>
</td>
<td style="background-color:#eeeeee;height:100px;width:200px;text-align:top;"> <ul> <li>The orders of magnitude established - ready to run simulations.</li> </ul>
</td> </tr>
</table> </html>
Day | Monday | Tuesday | Wednesday | Thursday | Friday |
---|---|---|---|---|---|
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:200px;text-align:top;"> <ul>
<li>Implementing the constant ranges in the output model.</li> <li>Comparing the results between the models.</li </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;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>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;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>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;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>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;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:200px;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:200px;text-align:top;"> <ul> <li>We got rid of the oscillations in our model (by using ode15s instead of ode45).</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> <ul> <li>Presentation ready.</li> <li>Reading on stiff equations done.</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> <ul> <li>Key sensitive parameters determined.</li> <li>Experiments initially discussed with Chris.</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;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 |
---|---|---|---|---|---|
Date | 16 | 17 | 18 | 19 | 20 |
Objective | Implementing the constant ranges in the output model. Comparing the results between the models. |
|
|
|
|
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). |
|
|
|
Week 8
<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:200px;text-align:top;"> <ul>
<li>Test the protein display model and find to what kind of values it's sensitive to.</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> <ul> <li>Define the control volume around the bacterial cell.</li> <li>Start on testing the model.</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> <ul> <li>We realised that it would be worth adding the last step (colour production by dioxygenase) into our amplfication models.</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> <ul> <li>We need to finalise testing and formulation of certain assumptions regarding the amplfication (cell death in particular).</li> <li>Consider helping RMIT- Australia in modelling.</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> <ul> <li>Keep exploring the prospective solutions to our system going unstable.</li> <li>Try to implement the last bit of amplification in TinkerCell. Maybe it will deal with it well.</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:200px;text-align:top;">
<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> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> <ul> <li>Control volume defined.</li> <li>Testing of model done.</li> <li>Protein model pretty much finalised.</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> <ul> <li>The colour production almost complete, however complications were encountered regarding the cell death (colour compound slowly kills cells).</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> <ul> <li>Basically we're stuck: scaling didn't help neither did trying idfferent solvers.</li> <li>Meeting with Matthieu gave us some prospective solutions that we can explore.</li> <li>Alternatively we can have a look at SimBiology or MatCont.</li> <li>Helping RMIT: their request is for protein engineering simulation - we cannot do that</li> </ul>
</td>
<td style="background-color:#eeeeee;height:200px;width:200px;text-align:top;"> <ul> <li>We know how to use the ''splinetool'' in Matlab.</li> <li>Specifying the time span helps to reduce the simulation time.</li> <li>Model was implemented in TinkerCell.</li> <li>Increasing relative or absolute tolerance in Matlab prevents some solutions from going negative. The key point is that we are only interested in the first few minutes of the experiment as the reaction to catechol is really quick.</li> </ul>
</td> </tr>
</table> </html>
Day | Monday | Tuesday | Wednesday | Thursday | Friday |
---|---|---|---|---|---|
Date | 23 | 24 | 25 | 26 | 27 |
Objective | Test the protein display model and find to what kind of values it's sensitive to |
|
|
|
|
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. |
|
|
|
|
Week 9
Day | Monday | Tuesday | Wednesday | Thursday | Friday |
---|---|---|---|---|---|
Date | 30 | 31 | 01 | 02 | 03 |
Objective | Bank holiday |
|
|
|
|
Completion |
|
|
|
Week 10
Day | Monday | Tuesday | Wednesday | Thursday | Friday |
---|---|---|---|---|---|
Date | 06 | 07 | 08 | 09 | 10 |
Objective | |||||
Completion |