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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.