Publications

Digital libraries (DL) are starting to play a central role in traditional libraries as well as becoming an important tool for publishers to present and sell their products. A lot of research has been carried out to study the usability and data representation in DL and has led to the development of a variety of software packages, both commercial and open source. However, very little research has focused on formal aspects of DL. This paper describes our attempt to formally specify DL using the RAISE Specification Language (RSL). The specification methodology, inspired by the 5S Framework defined by Gonccalves et al. [7], is kept at a fairly abstract level and aims to provide a basic model of the key DL issues (digital objects, collections, users and communities) as well as their relations within the DL framework and the implication of such relations in terms of security and human-computer interactions.

 We present a methodology for modelling population dynamics with formal means of computer science. This allows unambiguous description of systems and application of analysis tools such as simulators and model checkers. In particular, the dynamics of a population of Aedes albopictus (a species of mosquito) and its modelling with the Stochastic Calculus of Looping Sequences (Stochastic CLS) are considered. The use of Stochastic CLS to model population dynamics requires an extension which allows environmental events (such as changes in the temperature and rainfalls) to be taken into account. A simulator for the constructed model is developed via translation into the specification language Maude, and used to compare the dynamics obtained from the model with real data.

Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform computerised simulations of biological systems, which are called in silico experiments, to attain important insights and predictions about the system behaviour with a considerably lower cost. Computer visualisation is an important part of this approach, since it provides a realistic representation of the system behaviour. We define a formal methodology to model biological systems using different levels of representation: a purely formal representation, which we call molecular level, models the biochemical dynamics of the system; visualisation-oriented representations, which we call visual levels, provide views of the biological system at a higher level of organisation and are equipped with the necessary spatial information to generate the appropriate visualisation. We choose Spatial CLS, a formal language belonging to the class of Calculi of Looping Sequences, as the formalism for modelling all representation levels. We illustrate our approach using the budding yeast cell cycle as a case study. 

This paper describes preliminary results on the application of statistical model-checking to systems described with Stochastic CLS. Stochastic CLS is a formalism based on term rewriting that allows biomolecular systems to be described by taking into account their structure and by allowing very general events to be modelled. Statistical model-checking is an analysis technique that permits properties of a system to be studied on the results of a number of stochastic simulations. We choose Real-Time Maude as a tool that supports the modelling and analysis of systems with real-time properties. We adapt Gillespie's algorithm for simulating chemical systems into our approach. The resulting method is applied to analyse some simple examples and a model of the lactose operon regulation in E.coli.

 This article describes a framework to formally model and analyse human behaviour. This is shown by a simple case study of a chocolate vending machine, which represents many aspects of human behaviour. The case study is modelled and analysed using the Maude rewrite system. This work extends a previous work by Basuki which attempts to model interactions between human and machine and analyse the possibility of errors occurring in the interactions. By redesigning the interface, it can be shown that certain kinds of error can be avoided for some users. This article overcomes the limitation of Basuki’s approach by incorporating many aspects of user behaviour into a single user model, and introduces a more natural approach to model human–computer interaction.