IGEM:Imperial/2010/Objectives: Difference between revisions
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! Day !! Monday !! Tuesday!! Wednesday !! Thursday !! Friday | ! Day !! Monday !! Tuesday!! Wednesday !! Thursday !! Friday | ||
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| Date || 30 || 31 || 01 || 02 || 03 | | Date || 30 || 31 || 01 || 02 || 03 | ||
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| Objective | | Objective | ||
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* compare the catechol colour response (cells alive vs. immediate cell death) | * compare the catechol colour response (cells alive vs. immediate cell death) | ||
* discuss with Matthieu on the issue of negative concentrations, volume approximations made in protein display model and the idea of modelling the false positive case | * discuss with Matthieu on the issue of negative concentrations, volume approximations made in protein display model and the idea of modelling the false positive case | ||
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*Update Modelling section of the Wiki | |||
*Update list of experiments (especially for Protein Display Model) and discuss with Chris and Wolf | |||
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| Completion || || | | Completion || || | ||
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*SimBiology package generates same graphs as our manual simulations. The interface is quite easy to use. | *SimBiology package generates same graphs as our manual simulations. The interface is quite easy to use. | ||
*Decreasing absolute and relative tolerances is becoming accpeted as a solution to a negative concentrration problem (tomorrow there will be one more discussion on that with Matthieu) | *Decreasing absolute and relative tolerances is becoming accpeted as a solution to a negative concentrration problem (tomorrow there will be one more discussion on that with Matthieu) | ||
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Revision as of 03:07, 2 September 2010
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
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 | Date | 30 | 31 | 01 | 02 | 03 | |
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Objective | Bank holiday |
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Completion |
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Week 10
Day | Monday | Tuesday | Wednesday | Thursday | Friday | Weekend |
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Date | 06 | 07 | 08 | 09 | 10 | 11-12 |
Objective | ||||||
Completion |