Title: A Framework for Exploring Biology

Lecturer: Prof. Dr. Grzegorz Rozenberg

Period: June 16 - June 27, 2014  --- Sala riunioni Ovest: 11-13

In this series of lectures we present a framework for exploring biology which consists of:

  1. A STATIC part which is a depository of knowledge formalized by the notion of an extended zoom structure. The integrating structure of such a depository allows one to deal with the hierarchical nature of biology.
  2. A DYNAMIC part given by a family of reaction systems. They originated as models for processes instigated by the functioning of  living cells, and they address two important aspects of biology: non-permanency of its entitities and open system aspect of biological units such as living cells.

In this setup the depository of static knowledge given by an extended zoom structure is
explored by computations/processes provided by reaction systems, where this exploration can use/integrate knowledge present on different levels (e.g., atomic, cellular, organisms,
species, .... levels).

Research topics in this framework are motivated by biological considerations as well as
by the need to understand the underlying structure of knowledge as well as the
structure of computations exploring this knowledge. The models we discuss turned out to be
novel and attractive also from the theory of computation point of view.

The lectures are of interest to mathematicians and computer scientists interested
in formal models of computation and in modelling biological processes as well as to
bioinformaticians, biochemists, and biologists interested in foundational/formal understanding of biological processes. They are of a tutorial style and self-contained. In particular, no prior knowledge of biochemistry or cell biology is required.

The presented  framework was developed jointly with A. Ehrenfeucht from University of
Colorado at Boulder