Matlab Documentation

Inputs

The inputs to the model are the measurement tables of concentration of dye vs. time. Optional inputs to the model include an in vitro measurement of saturation of the dye, and measurements of the fluorescence of the dye with mRNA and protein synthesis turned off. The first optional measurement can be used to compare the in vitro fluorescence saturation levels with the in vivo fluorescence saturation levels in order to give a scaling factor for the all the measurements in the input. Estimations can be used in place of these to simplify the number of inputs. The second optional measurement can be used to determine the degradation rates of mRNA and protein.

Walkthrough

Fluoro2.m

This function is the function that is called to run the entire program. In addition, it takes the mRNA titration tables (modeldata) and converts it into fluorescent mRNA concentrations. It then passes the degradation data to the degradation functions, Degradation.m and DegradationP.m to return alpha2 and beta2, the degradation coefficients.

Degradation.m

This function takes in mRNA fluorescence data with mRNA synthesis turned off. This makes determining degradation rates easier, as all the change (as we will define degradation) in the mRNA concentration will be due to degradation. The function takes the data and fits a curve to the data, in the process calculating the degradation rate.