Minnesota/1 July 2009

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A major issue was uncovered with the model being used. Specifically, designGUI, when deleting reactions, will delete unused species, which is good. The GUI though also does not update which species number is being "Split on Division" (SOD). This resulted in RNAp being split every time the cells divided. Since it wasn't being produced, the number of RNAp per cell would continue to decrease as time went on, which would result in lower GFP production than expected.

Today I ran the base model after checking to make sure, finally, that everything was as it was expected to be, including the species being split on division:


Reaction Forward Kinetic Constant Reverse Kinetic Constant
RNAp + tetO1:tetR2 + lacP -> RNAp:lacP + tetR2623000
RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR2623000
RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR2623000

In this model, the constant was increased drastically to 6.23E+05, which definitely decreases the leakiness of the model. However, the model still shows a hump, which is definitely incorrect.