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Minnesota/25 June 2009
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| + | '''Patrick'''<br> | ||
| + | I got back the analysis of the models submitted yesterday. I submitted a base model shown here:<br> | ||
| + | |||
| + | <center><gallery widths=400 heights=300> | ||
| + | Image:badBase.jpg|Figure 1 - Base TTN Model | ||
| + | </gallery></center><br> | ||
| + | |||
| + | I also changed the tendency for tetO1 to detach from the tetR2:tetO1:2aTc complex (k=100000 1/s initially) by lower or higher an order of magnitude:<br> | ||
| + | |||
| + | <center><gallery widths=300 heights=200> | ||
| + | Image:badk2u.jpg|Figure 2 - Increased Rate of tetO1 Detachment from tetR2:tetO1:2aTc complex | ||
| + | Image:badk2d.jpg|Figure 3 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:2aTc complex | ||
| + | </gallery></center><br> | ||
| + | |||
| + | <center><gallery widths=300 heights=200> | ||
| + | Image:badk2u.jpg|Figure 4 - Increased Rate of tetO1 Detachment from tetR2:tetO1:aTc complex | ||
| + | Image:badk2d.jpg|Figure 5 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:aTc complex | ||
| + | </gallery></center><br> | ||
| + | |||
| + | <center><gallery widths=300 heights=200> | ||
| + | Image:badk12u.jpg|Figure 6 - Increased Rate of tetO1 Detachment from tetR2:tetO1:2aTc/aTc complex | ||
| + | Image:badk12d.jpg|Figure 7 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:2aTc/aTc complex | ||
| + | </gallery></center><br> | ||
| + | |||
| + | None of the graphs were particularly interesting. I also submitted two more jobs: '''smad_tetRu/d''' which either increased or decreased the rate of synthesis of tetR2 (reaction 44, k = 1E-11 M/s initially) by an order of magnitude.<br> | ||
| + | |||
| + | '''Ben'''<br> | ||
In order to try to improve the model, the following reaction constants were changed to try to see less leakiness in the model. | In order to try to improve the model, the following reaction constants were changed to try to see less leakiness in the model. | ||
<br> | <br> | ||
Latest revision as of 22:04, 30 July 2009
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Patrick
I got back the analysis of the models submitted yesterday. I submitted a base model shown here:
 Figure 1 - Base TTN Model |
I also changed the tendency for tetO1 to detach from the tetR2:tetO1:2aTc complex (k=100000 1/s initially) by lower or higher an order of magnitude:
 Figure 2 - Increased Rate of tetO1 Detachment from tetR2:tetO1:2aTc complex |
 Figure 3 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:2aTc complex |
Figure 4 - Increased Rate of tetO1 Detachment from tetR2:tetO1:aTc complex |
Figure 5 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:aTc complex |
 Figure 6 - Increased Rate of tetO1 Detachment from tetR2:tetO1:2aTc/aTc complex |
 Figure 7 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:2aTc/aTc complex |
None of the graphs were particularly interesting. I also submitted two more jobs: smad_tetRu/d which either increased or decreased the rate of synthesis of tetR2 (reaction 44, k = 1E-11 M/s initially) by an order of magnitude.
Ben
In order to try to improve the model, the following reaction constants were changed to try to see less leakiness in the model.
| Reaction | Forward Kinetic Constant | Reverse Kinetic Constant |
|---|---|---|
| RNAp + tetO1:tetR2 + lacP -> RNAp:lacP + tetR2 | 1200000 | |
| RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR2 | 1200000 | |
| RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR2 | 1200000 |
This model does indeed show some different leakiness, which is definitely a good thing, although the leakiness is still too high for an accurate model. Still, the problem remains where the model peaks and decreases instead of reaching a steady state.
