Biology Reference
In-Depth Information
Quantitative Modeling of Biochemical
Networks
R. Hofestadt
a
,∗
and S. Thelen
b
a
University of Magdeburg, Department of Computer Science, Magdeburg, Germany
b
University of Bonn, Department of Computer Science, Bonn, Germany
ABSTRACT:
Today different database systems for molecular structures (genes and proteins) and metabolic pathways are
available. All these systems are characterized by the static data representation. For progress in biotechnology, the dynamic
representation of this data is important. The metabolism can be characterized as a complex biochemical network. Different
models for the quantitative simulation of biochemical networks are discussed, but no useful formalization is available. This
paper shows that the theory of Petrinets is useful for the quantitative modeling of biochemical networks.
KEYWORDS:
Bioinformatics, biochemical networks, modeling and simulation, petrinets
INTRODUCTION
Methods of biotechnology allow the analysis of biochemical reactions and the isolation, sequencing,
analysis, and synthesis of genes and proteins [1]. This opens a wide area of applications and will produce
various changes in science and human behavior. However, in medicine new drugs could be designed
by using these data methods of biotechnology and biocomputing [2]. To make this technology more
useful, enormous efforts are necessary. The dream of drug design and gene therapy can become reality,
if interdisciplinary efforts are successful. Therefore, the phenomena of gene regulation and the modeling
of biochemical reactions has to be analyzed [3]. The new research area, that tries to solve these problems,
is called metabolic engineering [4,5]. The goal of this research field is to develop and implement tools
in practice and theory which will carry out the analysis and synthesis of metabolic engineering. In
the case of theoretical parts, bioinformatics has already developed different tools to accomplish this
version. However, database systems for genes (EMBL, GENBANK) and proteins (PIR, SWISSPROT)
are available
via
Internet. Moreover, the Boehringer company is collecting the data of all analyzed
biochemical reactions. This data is presented by the Boehringer pathway chart [6]. Since the beginning
of 1997 the electronic representation of the biochemical pathways is available via internet [7]. The main
gap is still the dynamic representation of these molecular data. Different models and simulation shells
are developed, but this gap still exists [8].
∗
Corresponding author: R. Hofestadt, Otto-von-Guericke-Universitat Magdeburg, Institut fur Technische und Betriebliche
Informationssysteme, AG/Bioinformatik und Medizinische Informatik, Universitatsplatz 2, D-39106 Magdeburg, Germany.
E-mail:
hofestaedt@iti.cs.uni-magdeburg.de
.
