Kasey E. O'Connor Week 14 Journal

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Creating The Model Input File

To create the Input file we will be using to run the program in MatLab, I used the sample file that was uploaded by Dr. Fitzpatrick, and made the correct adjustments for our data. I began by inserting the transposed regulation matrix from YEASTRACT into the network, network weights, and network thresholds sheets. For organizational purposes, I put all of the genes into alphabetical order. Because I am looking at the effects of a deleted GLN3, that row and column had to be deleted from the matrix. I then had to go to YEASTRACT and get all of the systematic names for the genes since we were only given the standard names. Using the protein half-life data from a paper by Belle et al. (2006) I filled in the degradation rates, as well as the production rates, which are just 2 times the degradation rate. However, the paper did not have data for HMO1, HOT1, and MGA2, so I used 0.027182242 given by Dr. Dahlquist. After, I had to consult the Week 9 spreadsheet to get the Average Log Fold Change and the standard deviation for times 15, 30, and 60. These were inputed into their respective worksheets for each gene. Lastly, I changed the stimulation times to increase by increments of 5 from 0 to 60. This spreadsheet is now ready to be run through the MatLab program to obtain the estimate values for the parameters.

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