ChemokineSwitch

This repo contains the code for the boolean model described in 'A Putative “Chemokine Switch” that Regulates Systemic Acute Inflammation in Humans'.

Getting Started

To get a local copy up and running follow these simple steps.

Prerequisites

• Python 2.7

• BooleanNet 1.2.8

  pip install booleannet==1.2.8

• Navigate to the folder where booleannet was installed and fix an error in network.py (See this open issue)

  sed -i 's/from networkx import component/from networkx import components/g' /path/to/boolean2/network.py

• pandas

  pip install pandas

Installation

1. Clone the repo

   git clone https://github.com/nazhar/ChemokineSwitch.git

Usage

The folder 'model_rules' contains text files for different versions of the model created during the model building process. To run simulations for each of these models:

python sim.py

This creates a directory named 'model_output' and writes csv files with the simulation results.

A short R script plot_sim_results.R is also included for plotting the results in figures similar to the ones in the paper.

To generate a state transition diagram for each of the models for both moderate and severe injury:

python state_transition.py

This will write '.gml' files for each model and injury severity which can then be viewed in your favorite graph viewer. The figures in the paper were generated using yEd

Figures 2 and 3 from the paper were generated using Model B. Figures 3-5 and the Figure S3 were generated using Model C. Model E explores the behavior if the mutual repression between chemokines was removed.

This repo may be update with a docker image for easier setup in the future.