Investigating the two regimes of fibrin clot lysis: an experimental and computational approach

  Investigating the two regimes of fibrin clot lysis: an experimental and computational approach Dataset and python files (Python3) to reproduce all figures and simulations presented in the manuscript.   ********************** * Run_simulations.py * ********************** * To run the simulations:   python3.8 Run_simulations.py arg1 arg2 arg3 arg4   - arg1:     Directory with experimental lysis profiles      - arg2:     Directory to store initial conditions of the lysis (i.e state of the system after clot formation)     if the directory does not exist, it is created.      - arg3:     Directory to store the simulated lysis profiles     if the directory does not exist, it is created.    - arg4:      index of the first set of clotting kinetic parameters (92 sets of parameters)    - arg5:      index of the last set of clotting kinetic parameters (92 sets of parameters) * Example: python3.8 Run_simulations.py Raw_Data/ Init/ Results/ 0 92 * Requires:   - module_fibrin_polymerization_Diamond_kinetics.py   - module_kinetics.py   - solid_Diamond_Anand_dict.py (dictionnary with parameters of the simulations)   - output_parameters_polymerization_T1000.txt (sets of clotting kinetic parameters)   - Mean_LAT_LYS_shell.txt (mean fraction of shells during slow and fast lysis for each experiment. Used to compute the distribution of shells for the surrogate model) **************************************** * make_analysis_figures_simulations.py * **************************************** * To reproduce the figures associated to simulation results:   python3.8 make_analysis_figures_simulations.py arg1 arg2 arg3 arg4   - arg1:   Directory with experimental lysis profiles   - arg2:   Directory with the simulated lysis profiles   - arg3:   Directory with initial conditions   - arg4:   Directory with the results of the sensitivity analysis * Example: python3.8 make_analysis_figures_simulations.py Raw_Data/ Results/ Init/ Sensitivity_Analysis/ * PDF Figures are created in the current directory * Requires:   - module_analyze_simulations.py   - module_analyze_data.py   - output_parameters_polymerization_T1000.txt   - manip_summary.txt (clot formation time, slow lysis time, fast lysis time for each experiment)   - Experiments_sorted.txt (experimental conditions, sorted by increasing order of concentrations) **************************************** * make_analysis_figures_experiments.py * **************************************** * To reproduce the figures associated to experimental results:   python3.8 make_analysis_figures_experiments.py arg1   - arg1:   Directory with experimental lysis profiles * Example: python3.8 make_analysis_figures_experiments.py Raw_Data/ * PDF Figures are created in the current directory * Requires:   - module_analyze_data.py   - Experiments.txt (contains experimental conditions)