Project:
Subproject: "Integrative simulation of gene controlled biochemical networks"
Grants (BMBF): 01KW9912 (01.11.1999-31.10.2002), 01KW0202 (01.11.2002-31.08.2004)
Project Leader:
- Ralf Hofestädt
Technical Faculty
Bielefeld University
hofestae (at) techfak.uni-bielefeld.de
Scientists:
- Niels Grabe
- Matthias Lange
- Thoralf Töpel
Background
Today we face a number of valuable data sources giving specialized views to highly specific aspects of biological systems ranging from genetic sequences up to pathological data. The same applies to the corresponding software where programs for analysis, modeling and simulation of individual aspects of biological data have been developed. These facts lead to the general task of integrating all this knowledge to make it biotechnologically and medically applicable.
Aim
The goal of our project is to implement an information system which supports the analysis of gene controlled biochemical networks. Using and enhancing existing methods of bioinformatics, we plan to integrate different biochemical, molecular and medical databases which are important for the analysis of metabolic diseases. A special data integration system, partially based on the design of federated database systems and on the prototype of our Biobench system will be designed. As a second step methods for integration of tools, simulating gene controlled biochemical networks will enhance this system and lead to an integrated server for gene controlled biochemical networks.
Method
Petrinet and rule-based simulation methods will be studied for modeling and simulation cellular signal pathways based on cell communication and gene regulation processes. Promoter detection methods will be used from the research partner T. Werner. Integration of databases will be done using FDBS techniques. While TRANSFAC contains knowledge about gene expression, biochemical reactions and signal pathways are supplied by KEGG and TRANSPATH. BRENDA stores behavior of enzymatic driven processes. For medical data METAGENE and MDDB are used. The simulation tools and databases will be combined into a gene regulation server accessible via web interface.
Result
The developed Internet server establishes a widely usable system concerning gene regulation starting on the mere sequence level up to pathological data. The project reshapes the currently available biomedical knowledge by integrating it, eases its understanding and thus opens up the road for exploiting it for medical and pharmaceutical research.
Links
- Information system for metabolic disorders MD-Cave
- Rare Metabolic Disease Database RAMEDIS
- German Human Genome Project