As the amount of biological data in the public domain grows, so does the range of modeling
and analysis techniques employed in systems biology. In recent years, a number of …

The aim of this chapter is to act as a primer for those wanting to learn about Runtime
Verification (RV). We start by providing an overview of the main specification languages …

Abstract The term Cyber-Physical Systems (CPS) typically refers to engineered, physical
and biological systems monitored and/or controlled by an embedded computational core …

Objective An innovative method based on topological data analysis is introduced for
classifying EEG recordings of patients affected by epilepsy. We construct a topological …

To express temporal properties of dense-time real-valued signals, the Signal Temporal
Logic (STL) has been defined by Maler et al. The work presented a monitoring algorithm …

Abstract Model checking together with other formal methods and techniques is being
adapted for applications to biological systems. We present a selection of approaches used …

Background Computational support is essential in order to reason on the dynamics of
biological systems. We have developed the software tool ANIMO (Analysis of Networks with …

Computational modeling can be used to investigate complex signaling networks in biology.
However, most modeling tools are not suitable for molecular cell biologists with little …

Understanding in silico the dynamics of metabolic reactions made by a large number of
molecules has led to the development of different tools for visualising molecular interactions …

Living cells are constantly subjected to a plethora of environmental stimuli that require
integration into an appropriate cellular response. This integration takes place through signal …