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.
The bioLQM tool provides automated modification (perturbation, booleanization, and reduction) and conversion of Logical Qualitative Models of biological networks. It can be used on the command line and provides a scripting API. It is also used as library to provide the core of the GINsim modelling tool.