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.

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* Run_simulations.py *
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* 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)

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* make_analysis_figures_simulations.py *
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* 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)

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* make_analysis_figures_experiments.py *
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* 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)