/percolation-grn

Code to reproduce the results of the paper "Percolation on the gene regulatory network"

Primary LanguageJupyter Notebook

Percolation on the gene regulatory network,

Giuseppe Torrisi et al J. Stat. Mech. (2020) 083501 https://doi.org/10.1088/1742-5468/aba7b0.

See this twitter thread for a short summary of what is in the paper.

This repository contins all the code to reproduce the figures of the paper. This repository requires:

  • Python version 3.6 or higher
  • Mathematica and wolframscript installed
  • jupyter notebooks

Each folder performs a task. Inside each folder, use the following order to execute files:

  1. *.wls
  2. *.py
  3. *ipynb

Also Section_4/macroscopic-cavity should be run first.

Content of the repository

  • lib: a folder with interal routines for python scripts

  • Section 3 contains a Mathematica notebook

  • Section 4 contains:

    • macroscopic-cavity: this folder compute the macroscopic cavity theory for type 1 networks.
    • pruning-aOC; percolation on synthetic network:
    • single-instance: microscopic cavity dynamics
    • knockout-cascade: single gene removal

  • Section 5 contains: strongly connected component evaluation.

Extensions for bipartite graphs in networkx

This repository relies heavily on networkx. Some method for direct bipartite graph generation have been extendend. In particular:

  • directed biparite random graph generation
  • configurational model for directed bipartite graph

Moreover in- and out-component are computed for directed graph. Go in the lib folder to know more