technical report BlenX for modelling and simulating living systems


Abstract

In the past, many scientists and philosophers have been inspired by the parallel between nature and human design, in mathematics and engineering. Today, the huge increase in biological knowledge, together with the developments in computer simulation modelling, and in design engineering systems, have made more comprehensive system-level studies of nature possible. The modern biological, medical, and pharmaceutical research approaches computing not only under the need of data mining and processing, but also under the need of using new languages for describing, designing and simulating biological entities and interactions. Although the techniques of the infinitesimal calculus have been recognized to provide valuable computational tools in simulating dynamic systems, they often do not offer the possibility to nimbly capture the intrinsic concurrency, causality, compositionality and probabilistic nature of biological interactions. This technical report presents the BlenX language, that has been recently developed at COSBI. BlenX is a programming language implementing the Beta-binders calculus. This calculus is a process algebra developed to model the time evolution of biological systems at any scale (from molecular to ecological systems). Namely, its syntactical and semantic structures have been specifically built to represent a biological entities and the network of its interactions with the other entities and components of a system. The richness and the level of abstraction of its syntax enable the modeler to describe through this calculus either the biochemical interactions between atom, molecules, functional complexes, cells, tissues at the micro- and meso-scale or the interactions and the relationships among the individuals of an ecological system. Some examples of application of BlenX to model living systems are given.



Paper Details

Authors

P. Lecca

Download

/var/papers/TR/TR-9-2010.pdf

Language

English
.