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

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