PPI network simulation under study bias

Simulates the measurement process of observed PPI networks under study bias as described in:

Blumenthal DB, Lucchetta M, Kleist L, Fekete SP, List M, Schaefer MH. Emergence of power-law distributions in protein-protein interaction networks through study bias. eLife. 2024;13:e99951. doi: 10.7554/eLife.99951.

• To generate the plots shown in the manuscript, execute the workflow in the notebook plot_results.ipynb.

• To reproduce the results of the simulation study, run the script_simulation.py as follows:

  python3 script_simulation.py

• The first part of the script generates parameter files (.json), which are saved in parameter_settings/all_param_combinations/ folder.

• The second part of the script reads the parameter files and runs the simulation for each set of parameters using parallel processing.

• The results are saved in output_results/ folder.

• Attention: Reproducing the results might take several weeks depending on the computational infrastructure.