Research Projects
BMBF Project: “Semi-automatic construction and visualization of complex metabolic networks based on the Petri net Concept“
Scientific objectives
The main goal of Systems Biology world-wide is to realize the implementation
of a virtual cell. However, the electronic
infrastructure for the realization of this fundamental idea does not yet exist.The
main goal of this cooperative project is
to develop and implement a tool for the semi-automatic implementation of complex
metabolic Petri nets. Therefore, we
have to implement a data integration tool, which will allow the automatic
access to relevant metabolic databases
(KEGG, BRENDA, TRANSFAC, TRANSPATH, BIND, etc.). Based on this integration
layer, we will implement a
visualization tool for complex metabolic networks and a Petri net transformation
tool, which is able to translate
selected metabolic networks into the language of Petri nets. In case of the
Petri net simulation, the outstanding Petri
net simulation tool Cell Illustrator will be integrated. Based on this tool,
we will test and evaluate the system using data
from rice (coming from the Chinese partner) and from crop (coming from IPK
Gatersleben).
Project description
Today, the visualization and simulation of complex metabolic networks is
of interest and importance for the future of
Biotechnology (Systems Biology). The idea of this project is to bring together
promising appendages coming from
database integration, visualization and simulation. All partners have developed
different tools. Prof. Hofestädt is an
expert in integration and Petri net simulation of networks. Prof. Schreiber
is an expert in the visualization of networks
and Prof. Chen has a strong background in pathway prediction and alignment.
By combining our tools and experience,
we are able to implement a powerful tool for the analysis of metabolic pathways
based on the Petri net analysis and
simulation. This tool can also be the backbone of a virtual cell simulator.
The realization of a virtual cell is the focus of
various national and international projects. Until now, no qualified theoretical
concept and tool could be presented.
Run time: 2008 - 2010
Project Members:
AG Bioinformatik
Prof. Ralf Hofestädt
IPK Gatersleben
Plant Bioinformatics Group
Prof. Dr. F. Schreiber
Dr. U. Scholz
www.nwg.bic-gh.de
Zhejiang University
College of Life Sciences
Prof. Dr. M. Chen
Prof. Dr. Wu
http://www.cls.zju.edu.cn/binfo