Finished the first draft of the model, will leave it until we have real data to feed back into the system. The model is very robust and allows any user to input a large variety of parameters and scenarios that could be realistically expected in the laboratory results. The output of the model is the colour that you can expect over time (the outputs of the real system will be from a combination of mCherry and GFP).

The model reveals surprising results, including how even a small basal rate of gene expression (due to leakage of the promoters) can really change the results.

The way that I finally got the model to work was by returning to the ODE15s function in Matlab and not bothering with Laplace transforms. Information on how to use Matlab to model repressor and activator networks very easily, accurately and quickly will be uploaded to this wiki soon! If you want more details please don't hesitate to contact us.

Today was difficult. It was spent trying to write Matlab code to solve the differential equations. Having already written

Help with the

autorepressor/autoactivator code

will be up on the wiki shortly, please don't hesitate to contact us in the meantime for more info though.

The morning was spent with Glen and Fran (who are working on part B) discussing exactly what network of activation and repression we were trying to categorize and turning it from Snapgene files (that the Biochemists understand) into a series of possible repression and activation scenarios.

Then, it was a matter of condensing the network of seemingly complex interactions into a set of differential equations with the relevant constants. This allows the response of the system to an external known input be accurately modeled.