Affiliations: Fraunhofer-Institute for Algorithms and Scientific
Computing (SCAI) [GMD], D-53754 Sankt Augustin, Germany | Computer Science Department, Brandenburg University of
Technology at Cottbus, D-03013 Cottbus, Germany | Department of Bioinformatics, Technical University of
Applied Sciences Berlin, D-13347 Berlin, Germany
Abstract: Computer assisted analysis and simulation of biochemical pathways
can improve the understanding of the structure and the dynamics of cell
processes considerably. The construction and quantitative analysis of kinetic
models is often impeded by the lack of reliable data. However, as the
topological structure of biochemical systems can be regarded to remain constant
in time, a qualitative analysis of a pathway model was shown to be quite
promising as it can render a lot of useful knowledge, e.g., about its
structural invariants. The topic of this paper are pathways whose substances
have reached a dynamic concentration equilibrium (steady state). It is argued
that appreciated tools from biochemistry and also low-level Petri nets can
yield only part of the desired results, whereas executable high-level net
models lead to a number of valuable additional insights by combining symbolic
analysis and simulation.
