BoolSi: A Tool for Distributed Simulations and Analysis of Boolean Networks

Abstract

We present BoolSi, an open-source cross-platform command line tool for distributed simulations of synchronous Boolean networks. 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.

Keywords

• boolean networks
• mpi
• python
• bioinformatics
• gene regulatory networks