Here are the main software I am working on, as part of my research work. I also have some toy projects on GitHub.
GINsim provides a (tentatively) friendly graphical interface for the definition and analysis of logical models. I have been involved with its design and development since 2005.
Logical model toolkit
The LogicalModel tool converts logical models from one format to another. It is also used as library to provide the core of the GINsim modelling tool.