Improving the Timed Automata Approach to Biological Pathway Dynamics.

Biological systems such as regulatory or gene networks can be seen as a particular type of distributed systems, and for this reason they can be modeled within the Timed Automata paradigm, which was developed in the computer science context. However, tools designed to model distributed systems often require a computer science background, making their use less attractive for biologists. ANIMO (Analysis of Networks with Interactive MOdeling) was built with the aim to provide biologists with access to the powerful modeling formalism of Timed Automata in a user friendly way. Continuous dynamics is handled by discrete approximations. In this paper we introduce an improved modeling approach that allows us to considerably increase ANIMO's performances, opening the way for the analysis of bigger models. Moreover, this improvement makes the introduction of model checking in ANIMO a realistic feature, allowing for reduced computation times. The user interface of ANIMO allows to rapidly build non-trivial models and check them against properties formulated in a human-readable language, making modeling a powerful support for biological research.