Molecular Networks: from a formal description to a software tool

Gabriel
Ciobanu

Professor, Romanian
Academy
Institute of Computer Science

A system of interacting molecular entities
can be described and modeled by a system of communicating processes or
communicating automata. The pi-calculus is a useful abstraction for biomolecular systems, particularly to provide a qualitative
description. In order to include quantities, we use a network of communicating
automata, and provide some theoretical results. This formal model can provide a
detailed description of the biological system, and its implementation is able
to deal with large amounts of data. We use our software tool to simulate and analyze the T cell behaviour.
Links to a recent approach in the mathematical theory of modeling and
simulation can help and improve the biological software experiments.