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Robustness and Plasticity in Regulatory Networks

The BoolNetPerturb package adds functions to BoolNet for perturbing Boolean Regulatory Networks. This functions can be used for the study of biological systems. This package is capable of labeling states, simulating multiple knock-outs and over-expressions and simulating fixed and transient perturbations in the states and trajectory of a network. See the Jupyter Tutorials for more examples.

Installation

Using devtools in R:

install.packages("devtools")
library(devtools)
install_github("mar-esther23/boolnet-perturb")

You can also install from source:

Download code from github and unzip.

Or clone the repository:

git clone https://github.com/mar-esther23/boolnet-perturb.git

In R run:

install.packages(path_to_file\boolnet-perturb, repos = NULL, type="source")

You can see the tutorials in github, but if you want to run them you need Jupyter and the Rkernel.

Jupyter Tutorials

  • Introduction
    • Robustness in biological systems
    • Boolean regulatory networks
    • Biological system: Th17/iTreg network
  • BoolNet
    • Installation
    • Construction
    • Attractors
    • Labels
  • Functions
    • Over-expression and knock-outs
    • Fixed environments
    • Truth tables
  • Updating
    • Synchronous vs asynchronous
    • Transition table
  • States and trajectories
    • Transient perturbations
    • Stochastic noise
  • Appendix
    • Simulation and model checking
    • Importing and exporting with SBML-qual

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