Minnesota/25 June 2009

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|'''[[Minnesota/24 June 2009|Go to Previous Day (June 24)]]'''|| width=158|'''[[Minnesota/26 June 2009|Go to Next Day (June 26)]]'''
|'''[[Minnesota/24 June 2009|Go to Previous Day (June 24)]]'''|| width=158|'''[[Minnesota/26 June 2009|Go to Next Day (June 26)]]'''
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'''Patrick'''<br>
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I got back the analysis of the models submitted yesterday. I submitted a base model shown here:<br>
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<center><gallery widths=400 heights=300>
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Image:badBase.jpg|Figure 1 - Base TTN Model
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</gallery></center><br>
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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>
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<center><gallery widths=300 heights=200>
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Image:badk2u.jpg|Figure 2 - Increased Rate of tetO1 Detachment from tetR2:tetO1:2aTc complex
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Image:badk2d.jpg|Figure 3 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:2aTc complex
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</gallery></center><br>
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<center><gallery widths=300 heights=200>
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Image:badk2u.jpg|Figure 4 - Increased Rate of tetO1 Detachment from tetR2:tetO1:aTc complex
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Image:badk2d.jpg|Figure 5 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:aTc complex
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</gallery></center><br>
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<center><gallery widths=300 heights=200>
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Image:badk12u.jpg|Figure 6 - Increased Rate of tetO1 Detachment from tetR2:tetO1:2aTc/aTc complex
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Image:badk12d.jpg|Figure 7 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:2aTc/aTc complex
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</gallery></center><br>
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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>
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'''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>
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! Reverse Kinetic Constant
! Reverse Kinetic Constant
|-
|-
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|RNAp + tetO1:tetR2 + lacP -> RNAp:lacP + tetR2||311000||
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|RNAp + tetO1:tetR2 + lacP -> RNAp:lacP + tetR2||1200000||
|-
|-
-
|RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR2||311000||
+
|RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR2||1200000||
|-
|-
-
||RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR2||311000||
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||RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR2||1200000||
|}
|}
<br>
<br>
[[Image:Tnnatcvariesleaky5.jpg|480px]][[Image:Tnnexperiment.jpg|480px]]<br>
[[Image:Tnnatcvariesleaky5.jpg|480px]][[Image:Tnnexperiment.jpg|480px]]<br>
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<br>
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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.

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:


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:




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 + tetR21200000
RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR21200000
RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR21200000


Tnnatcvariesleaky5.jpgTnnexperiment.jpg

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.