Research Projects
BMBF Project: "Prediction and reconstruction of metabolic networks based on textmining methods"
The cooperation between Prof. Kolchanov and Prof. Hofestädt has become a long tradition. Since 1998 we have various different seminars, workshops and summer schools together. One highlight of this cooperation is the foundation of the German/Russian network mentioned above. Furthermore, since 2000 Prof. Hofestädt has been the co-Chairman of the BGRS conference, which is organized regularly in Novosibirsk (next conference will be June 2008).
Reading the textbook of Prof. Ratner (Novosibrisk) Prof. Hofestädt began to model metabolic networks based on formal languages at the beginning of the 80’s (as a student). His Phd thesis and his Habilitation were based on the idea to use formal languages for the description of metabolic processes and networks. During the second half of the 90’s, when Prof. Hofestädt was Professor at the University of Magdeburg, he worked more closely with Prof. Kolchanov. Molecular databases and integration was becoming more and more the topic of our research. Both of us developed different database systems and started to develop integration tools for the automatic access and integration of molecular data. One result of the activities in Novosibirks is the ANDVisio tool, which we would like to further develop togehter in this project.
Bioinformatics, Systems Biology and Biotechnology are highly supported by DFG, BMBF and other national and international Foundations (VW-Stiftung etc.). However, we can see the same situation in Russia. During the last three years Prof. Hofestädt and Prof. Kolchanov founded the German/Russian Network Computational Systems Biology. All these activities were supported by BMB, Russian Ministry of Science and different other Partners.
The future of Biotechnology and Molecular Biology will be strongly affected by the development of Bioinformatics and Systems Biology. Today the implementation of tools for the user specific integration of databases, analysis tools and information systems is the most important topic of Bioinformatics and Systems Biology. Already in the world wide web we can see more than 1000 molecular information systems representing information about genes, proteins, enzymes, pathways, etc. Behind these database systems thousands of analysis tools are available in the internet. Based on these information systems and analysis tools the user is looking for integrative tools, which will help to realize the user specific application of selected databases and analysis tools.
The goal of our project seeks to offer a system, which is able to predict and analyse complex metabolic networks based on database integration and textmining tools.
Therefore, we will systematically extend the ANDVisio tool. One point is the user interface and the other is to use methods of deductive databases to support the automatic generation of new molecular knowledge. For the user interface we would like to implement a 3D visualisation tool for the analysis of predicted metabolic networks. For the generation of new knowledge we would like to implement a rule based systems for the automatic generation of metabolic networks.
We plan to cooperate from the beginning with Prof. Thiele (Bruker). He is also member of the German/Russian Network of Computational Systems Biology and interested in the results of this project. Few weeks ago Prof. Kolchanov presented ANDVisio in Bremen. Furthermore, we discussed the ideas of this project together in Bielefeld.
Run time: 2008 - 2009
Project Members:
AG Bioinformatik
Prof. Ralf Hofestädt
Dipl.-Inform. David Braun
Dipl.-Inform. Thorben Wallmeyer
M.A. Björn Sommer