Function list

• initializeNotebook - Generates folder structure for the current enzyme module;

• importAllData - Imports and formats data from the specified data notebook for the current enzyme module;

• printEnzymeData - Prints the final data to be used in the fit, including culling data that had a priority score of set by the user;

• constructEnzymeModule - MASS Toolbox function to take in a user-specified reaction mechanism and construct an enzyme module object;

• setUpRateEquations- Takes in an enzyme module object and generates steady-state equations used in fitting;

• simulateData - Takes in the data to be fit and generates comparison data curves to be used in the fitting;

• definePSOparameters - Specifies user parameters for the Particle Swarm Optimization algorithm;

• defineLMAparameters - Specifies user parameters for the Levenberg-Marquardt Algorithm;

• runFit - Generates and executes command line code to run the PSO and LMA optimization to fit the enzyme module to data;

• getRatesWithSSD - Imports optimized rate constants and recalculates the model target values;

• backCalculateKms - Utilizes the steady-state rate equations and fit microscopic rate constants to recalculate the macroscopic Km for the current enzyme;

• backCalculateKcats - Utilizes the steady-state rate equations and fit microscopic rate constants to recalculate the macroscopic kcat for the current enzyme;