Software tools

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

bioLQM: 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

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

Genetic Network Analyzer (GNA)

Genetic Network Analyzer (GNA) is a computer tool for the qualitative modeling, analysis, and simulation of gene regulatory networks

GINsim

Java software for the construction and analysis of multivalued models

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