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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.

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