Biology Reference
In-Depth Information
Petri Nets and the Simulation of Metabolic
Networks
Ralf Hofestadt
Bioinformatics/Medical Informatics, Technische Fakult at, Universit at Bielefeld, Postfach 10 01 31, D-33501
Bielefeld, Germany
E-mail:
ralf.hofestaedt@uni-bielefeld.de
Based on the Human Genome Project, the new interdisciplinary subject of Bioinformatics has become
an important research topic during the last decade. An important catalytic element of this process is that
methods of molecular biology (DNA-sequencing, proteomics etc.) allow the automatic data generation
of cellular components. Based on this technology roboter systems allow to sequence small genomes in
a few weeks. Moreover, the semi-automatic assembly and annotation of the sequence data can only be
done using methods of computer science. The molecular data is stored in database systems available
via the Internet. Based on that data, different questions can be solved using specific analysis tools.
Regarding the DNA sequences we are looking for powerful software tools which will predict functional
units in the DNA. Today this topic is called “From Sequence to Function” or “Post-Genomics”.
The common definition of Bioinformatics addresses the application of methods and concepts of
computer science in the field of biology. Bioinformatics currently stresses three main topics. The
first major topic is sequence analysis or genome informatics. Its basic tasks are: assembling sequence
fragments, automatic annotation, pattern matching and implementation of database systems, like EMBL,
TRANSFAC, PIR, RAMEDIS, KEGG etc. The sequence alignment problem is still representing the
kernel of sequence analysis tools. Nevertheless, sequence analysis is not a new topic. It was, and still is,
a topic of Theoretical Biology and Computational Biology. Protein Design is the second current major
research topic of Bioinformatics. The first task was to implement information systems that represent
knowledge about the proteins. Today many different systems, like PIR or PDB, are available. The main
goal of this research topic is to develop useful models which will allow the automatic calculation of
3D structures, including the prediction of the molecular behavior of this protein. Until now, molecular
modeling failed. Protein design is also not a new research topic. Its roots are coming from Biophysics,
Pharmaco Kinetics and Theoretical Biology. The third major topic is Metabolic Engineering. Its goal
is the analysis and synthesis of metabolic processes. The basic molecular information of metabolic
pathways is stored in database systems, like KEGG, WIT, etc. Models and specific analysis algorithms,
based on the molecular knowledge represented by these database and information systems, allow the
implementation of analysis tools.
The idea of Metabolic Engineering represents the basic idea of the Virtual Cell. Using molecular data
and knowledge, the implementation of specific models allows the implementation of simulation tools for
cellular processes. Behind the algorithmic analysis of molecular data, modelling and simulation methods
and concepts allow the analysis and synthesis of complex gene-controlled metabolic networks. The actual