BoolSi: a tool for distributed simulations and analysis of Boolean networks

TL;DR

BoolSi is an open-source tool enabling distributed simulation and analysis of Boolean networks, facilitating modeling of complex systems like gene regulatory networks with support for cluster and parallel processing.

Contribution

The paper introduces BoolSi, a novel cross-platform command line tool that supports distributed Boolean network simulations using MPI, with capabilities for attractor analysis and case studies.

Findings

Successfully modeled cambium cell activity

Enabled statistical analysis of network attractors

Supported execution on clusters and single computers

Abstract

We present BoolSi, an open-source cross-platform command line tool for distributed simulations of deterministic Boolean networks with synchronous update. It uses MPI standard to support execution on computational clusters, as well as parallel processing on a single computer. BoolSi can be used to model the behavior of complex dynamic networks, such as gene regulatory networks. In particular, it allows for identification and statistical analysis of network attractors. We perform a case study of the activity of a cambium cell to demonstrate the capabilities of the tool.