Comparison with other softwares for logic modeling. Adapted from. These methods can be distinguished by their treatment of state and time. CellNetAnalyzer uses steady state analysis of logic models to better understand signaling and regulatory networks . MetaReg  defines the prior knowledge of a system as a multi-state probabilistic model that can be simulated and visualized. BooleanNet  allows for synchronous and asynchronous simulations (as well as mixed approaches) and can also facilitate piecewise linear differential equations for a more detailed time resolution. BoolNet  also allows for synchronous and asynchronous simulations, and includes functionalities to deal with probabilistic Boolean networks where multiple transition functions can be chosen for each node. ChemChains is a software suite that allows for synchronous and asynchronous updating . GINsim offers a suite of simulations methods that incorporates a graph editor as well as various tools to explore state transitions . SQUAD  and Odefy  create continuous systems from logic models. Genetic Network Analyzer is a platform for modeling genetic regulatory networks, using piecewise linear models to model continuous processes . CellNOptR and its extensions (CNORfuzzy, CNORdt and CNORode) cover steady state discrete and continuous modeling in both state and time. Note that because multi-state is a generalization of binary, in principle all methods that handle multi-states also handle binary.
Terfve et al. BMC Systems Biology 2012 6:133 doi:10.1186/1752-0509-6-133