Software tools for logical modelling

The following software tools are developed by members of the CoLoMoTo consortium. This list is not exhaustive, please contact us to include new tools.

Java library for the manipulation and conversion of logical models R package for the simulation, reconstruction and analysis of various types of Boolean networks Web-based plateform for the construction and simulation of Boolean models A MATLAB package with graphical user interface for structural and functional analysis of cellular networks CellNOpt is a free open-source toolbox for creating logic-based models of signal transduction networks, and training them against high-throughput biochemical data.Simulation of epithelial patterning using multi-cellular multivalued logical models Java software for the construction and analysis of multivalued models Genetic Network Analyzer (GNA) is a computer tool for the qualitative modeling, analysis, and simulation of gene regulatory networks Java API library for parsing and writing SBML files and for in-memory manipulation of SBML data structures A comprehensive number of Python scripts that allow the specification, management and analysis of model pools Continuous time Boolean modeling Static analyzer for transient dynamics of automata networks Python API for the analysis of Boolean networks Standardized continous simulation of logical models Translates discretized time series data into LTL and CTL specifications for NuSMV model checking