The computer revolution in science: steps towards the realization of computer-supported discovery environments

THE MULTIAGENT TECHNOLOGY AND PARADIGM WITHIN SCIENTIFIC DISCOVERY

Scientific practice has been rapidly evolving in the last years under the pressure of developments in computer science and technology. In this paper we present some of the results of our research activity at the boundary between computer science and philosophy of science started in 1997 under Marco Somalvico's impulse and guidance. In particular, we discuss two roles that multiagent systems can play in scientific discovery. From the one hand, they can support scientific practice; from the other hand, they can represent scientific results. The theoretical framework presented in this paper is exemplified in concrete by illustrating specific implemented systems, both taken from the literature and developed by ourselves.

Modeling and simulation of genetic regulatory systems: a literature review

In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equations, stochastic equations, and rule-based formalisms. In addition, the paper discusses how these formalisms have been used in the simulation of the behavior of actual regulatory systems.