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We present an overview of the current status of the European collaborative
project PAEON. The challenge of PAEON is to provide specialists in reproduc-
tive medicine with a computerised model of the menstrual cycle under normal
and various pathological conditions, which will allow them to get further in-
sight in fertility dynamics. This model also enables the simulation of treatment
protocols, which were used within in vitro fertilization. By the definition of
virtual patients through biologically admissible parametrizations our approach
allows not only the evaluation of a given treatment strategy in silico, but also
the design and optimization of such protocols. Once a protocol is formalized
in the virtual hospital, the success can be controlled by a treatment execution
monitor, which works then as a clinical decision support system. All these tools
will be combined in a virtual hospital environment, enabling the access to the
PAEON services through the web.
Modelling, parameter identification, and simulation play an important rôle in Systems Biology. In recent years, various software packages have been established for scientific use in both licencing types, open source as well as commercial. Many of these codes are based on inefficient and mathematically outdated algorithms. By introducing the package BioPARKIN recently developed at ZIB, we want to improve this situation significantly. The development of the software BioPARKIN involves long standing mathematical ideas that, however, have not yet entered the field of Systems Biology, as well as new ideas and tools that are particularly important for the analysis of the dynamics of biological networks. BioPARKIN originates from the package PARKIN, written by P.Deuflhard and U.Nowak, that has been applied successfully for parameter identification in physical chemistry for many years.