GINsim

GINsim is a Java application for the construction and analysis of multi-valued logical models.

GINsim provides a user-friendly graphical interface to define the model itself. A collection of import and export filters enables the exchange of models with other tools (beside SBML qual, it supports some Petri net and model-checker formats).

GINsim supports the simulation of logical models by generating state transition graphs for synchronous and asynchronous updating modes, as well as piority classes.

Beside simulation, GINsim offers efficient methods for the determination of stable states without exploring the STG, as well as for the analysis of regulatory circuits associated to crucial dynamical properties.

Logical modelling of regulatory networks with GINsim 2.3
A. Naldi, D. Berenguier, A. Fauré, F. Lopez, D. Thieffry, C. Chaouiya (2009)
BioSystems 97:134-9 [doi:10.1016/J.Biosystems.2009.04.008] [pubmed:19426782]

Implemented methods

Identification of stable states

Asynchronous updating policy Updating policy relying on strict priorities Synchronous updating policy

Graph representing alternative trajectories

Supported formats

XML format used by GINsim Exchange format for logical models based on SBML