Figure 5

Comparison with other softwares for logic modeling. Adapted from[19]. 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[24]. MetaReg[25] defines the prior knowledge of a system as a multi-state probabilistic model that can be simulated and visualized. BooleanNet[26] 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[27] 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[28]. GINsim offers a suite of simulations methods that incorporates a graph editor as well as various tools to explore state transitions[29]. SQUAD[30] and Odefy[31] 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[32]. 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.