Spring 2014 Computational Journal

March 20, 2014

• Ran the Michaelis-Menten simulation using solely the dZAP1 data in order to produce the MAT file necessary to output graphs that compare the sigmoid and Michaelis-Menten models for dZAP1.
• It might be beneficial to consider putting a line in estimation_driver.m that specifies if one strain will be run or multiple strains. Otherwise, as the code is written now, multiple models and multiple sets of graphs (one for each strain) are produced even when a one strain simulation is run (by setting qq = 1 in general_least_squares_error.m).

March 28, 2014

Began merging the different scripts for the sigmoid and Michaelis-Menten deterministic models.

• In the "optimization_parameters" spreadhseet in the input workbook, added a row with the header Sigmoid. There is a 1 if a sigmoid model is to be computed or a 0 if the Michaelis-Menten model is to be determined.
• At the point in Parameters.m where the network thresholds b are imported as a vector bvec, changed the command to the following for loop to fix problems with exporting the network b's to the output in Excel:

if Sigmoid == 1
   [bvec,TX6]    = xlsread(input_file,'network_b');
   b = bvec;
end 

• In LSE, altered the for loop to do the forward simulation by putting in a switch between the scripts for the dynamics between the two models.
• In general_least_squares_error.m, altered the for loop to solve the differential equation to include a switch between the scripts for the dynamics between the two models.
• In output, created an if statement to output the network thresholds b only if the sigmoid model is being computed.

Katrina Sherbina 14:32, 28 March 2014 (EDT)