Fig 1.
Most relevant examples of computational modeling approaches introduced with toy examples.
Related tools are listed in Table 1. References for the examples are as follows: process algebras [12], compartment-based systems [21], rule-based systems [22], statecharts [23], hybrid systems [24], Boolean networks [25], Petri nets [26], agent-based models [27], lattice-based models [28].
Fig 2.
Comparison between the main features of the LTL (left) and Signal Temporal Logic (STL) (right) in terms of syntax (top), operators (middle), and semantics (bottom); the black circles represents a propositional state, and the arrows represent the next step in time.
Fig 3.
Summary of the features for the selected tools.
Tools are classified by the supported computational modeling language, their execution semantics, and the formal analysis that can be performed, based on the literature.
Table 1.
Summary of the main case studies in systems biology for the listed tools.