Matlab scripts to perform optimization and analyses of a dynamic optimization model of invasive aspergillosis: "Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis" Jan Ewald, Flora Rivieccio, Lukáš Radosa, Stefan Schuster, Axel A. Brakhage, Christoph Kaleta https://doi.org/10.1101/2021.05.12.443764 File structure: --- Core optimization files --- -- simulation.cpp -- Description of ODE model in 'C', used by solver to calculate the time course given the parameters, initial states and control variables -- simulation.mexa64 -- Compiled mex-File from simulation.cpp used as interface by MATLAB to 'C' files. -- optFun.m -- Definition of the objective function. Uses a control vector 'u' to calculate the, objective function value F, the time course of state variables 'x' and gradients used by the solver to determine the optimal control of 'u'. -- single_opt.m -- Function which performs an optimization run for a given parameter set and a randomized initial solution u0. Optimization can be conducted by SNOPT or in conjunction with IPOPT. Both solver are not provided here (proprietary). --- Additional files --- -- solve_with_ipopt.m -- Configuration file and interface to call the solver IPOPT. -- lognorm_mu.m -- Function to provide log-normal distributed samples given the standard deviation, reference value (mode of distribution) and number of samples which should be calculated. -- mice_param_alv.m -- Reference parameter set of the model for mice as host organism and cell numbers normalized per alveolus. -- parameter_model.m -- Definition of parameter container to handle interface to optFun-call by solvers which do not allow parameter in function call. --- Optimization Runs --- -- rand_params.m -- Performs optimization runs for multiple randomized parameter sets and several scenarios to determine parameter sensitivity. -- doseresponse.m -- Performs optimization runs for a sequnce of initial conidial dosages to determine the dose response of the system. --- Scripts for post-analysis --- -- rand_analysis.m -- Loads the data created by the optimization runs (rand_params.m) and performs parameter sensitivity analysis as well as produces plots for analysis related to parameter influence. -- doseanalysis.m -- Loads the data created by the optimization runs (doseresponse.m ) and produces dose response curves as well as additional plots and analyses. --- Optimization output files --- -- rand_param_out/ -- Folder contains optimization results as MATLAB session-file for randomized parameters used for parameter sensitivity analysis. -- dose_out/ -- Folder contains optimization results as MATLAB session-file for dose response curve calculation.