Fundamenta Informaticae - Volume 171, issue 1-4

Authors: Simone, Pernice | Laura, Follia | Gianfranco, Balbo | Luciano, Milanesi | Giulia, Sartini | Niccoló, Totis | Pietro, Lió | Ivan, Merelli | Francesca, Cordero | Marco, Beccuti

Article Type: Research Article

Abstract: Computational Biology is a fast-growing field that is enriched by different data-driven methodological approaches and by findings and applications in a broad range of biological areas. Fundamental to these approaches are the mathematical and computational models used to describe the different states at microscopic (for example a biochemical reaction), mesoscopic (the signalling effects at tissue level), and macroscopic levels (physiological and pathological effects) of biological processes. In this paper we address the problem of combining two powerful classes of methodologies: Flux Balance Analysis (FBA) methods which are now producing a revolution in biotechnology and medicine, and Petri Nets (PNs) which …allow system generalisation and are central to various mathematical treatments, for example Ordinary Differential Equation (ODE) specification of the biosystem under study. While the former is limited to modelling metabolic networks, i.e. does not account for intermittent dynamical signalling events, the latter is hampered by the need for a large amount of metabolic data. A first result presented in this paper is the identification of three types of cross-talks between PNs and FBA methods and their dependencies on available data. We exemplify our insights with the analysis of a pancreatic cancer model. We discuss how our reasoning framework provides a biologically and mathematically grounded decision making setting for the integration of regulatory, signalling, and metabolic networks and greatly increases model interpretability and reusability. We discuss how the parameters of PN and FBA models can be tuned and combined together so to highlight the computational effort needed to perform this task. We conclude with speculations and suggestions on this new promising research direction. Show more

Keywords: Computational biology, Petri Nets and Flux Balance Analysis

DOI: 10.3233/FI-2020-1888

Citation: Fundamenta Informaticae, vol. 171, no. 1-4, pp. 367-392, 2020

Authors: Umeo, Hiroshi

Article Type: Research Article

Abstract: The synchronization in cellular automata has been known as the firing squad synchronization problem (FSSP) since its development, in which it was originally proposed by Myhill and reported by Moore in 1964 to synchronize all/some parts of self-reproducing cellular automata. The problem has been studied extensively for more than fifty years, and a rich variety of synchronization algorithms has been proposed not only for one-dimensional (1D) arrays but also for multi-dimensional arrays. In the present paper, we construct a survey on the study of FSSP algorithms, focusing on recent developments.

Keywords: Cellular automaton, Firing squad synchronization problem, FSSP

DOI: 10.3233/FI-2020-1889

Citation: Fundamenta Informaticae, vol. 171, no. 1-4, pp. 393-419, 2020