BoolNet

Website: http://cran.r-project.org/web/packages/BoolNet

BoolNet is an R package for the construction and analysis of synchronous, asynchronous, probabilistic and temporal Boolean networks. It supports the simulation of such models, including the calculation and visualization of state transition graphs, basins of attractions and attractors. Networks can be reverse-engineered from measurements and imported from or exported to SBML qual. The package also provides methods for the robustness assessment of models and their comparison to randomly generated models.

BoolNet--an R package for generation, reconstruction and analysis of Boolean networks
C. Müssel, M. Hopfensitz, H.A. Kestler (2010)
Bioinformatics 26:1378-80 [doi:10.1093/Bioinformatics/Btq124] [pubmed:20378558]

Implemented methods

Asynchronous updating policy Synchronous updating policy

Graph representing alternative trajectories Stochastic exploration of alternative trajectories

Supported formats

Exchange format for logical models based on SBML