Freier, Andreas;Hofestädt, Ralf;Lange, Matthias - Object-oriented Modelling, Integration and Analysis of Gene Controlled Metabolic Networks

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Title: Object-oriented Modelling, Integration and Analysis of Gene Controlled Metabolic Networks	P38
Freier, Andreas; Hofestädt, Ralf; Lange, Matthias afreier@techfak.uni-bielefeld.de, hofestae@techfak.uni-bielefeld.de, lange@ipk-gatersleben.de Bioinformatics Group, Faculty of Technology, Bielefeld University and IPK Gatersleben

Our goal is the integrative computational construction and analysis o fgene controlled metabolic networks based on available data sources. Biochemical networks involve a huge number of nodes, whereat computational tools are needed to support the access to physically distributed databases, to integrate the heterogeneous data from these databases and to prepare the results of database integration in a way they can be processed by common analysis methods, e.g. simulation tools or visualization libraries. The analysis of integrated gene networks enables us to get an overview about topology and dynamics of cell process networks, the occurrence of biochemical objects and processes, the physical cell structures and characteristic cell profiles, e.g. the state of metabolic systems under conditions of metabolic diseases.

In our project MARG(*), we are developing a modular software platform (MARGBench)[2], applied to the topic of gene controlled metabolic networks. It contains modules for database integration, object-oriented (OO) modelling, visualization and simulation. The module IIUDB (System of Individually Integrated User Databases)[3]} has been developed to support the OO-modelling of biochemical networks directly from database integration. Modelling is done by defining object-oriented specifications, using standard modelling methods, e.g UML (Unified Modelling Language). Common modelling concepts, e.g. object abstraction and classication, inheritance, aggregation, association and modularity are used (see figure). The final specification includes a class diagram, defining object properties and the structure the OO-network. Processing this document, IIUDB creates a specific CORBA (Common Object Request Broker Architecture) environment providing
different object services, such as object storage and modification, object integration from
external sources, database queries and network analysis. For data integration, the MARGBench module BioDataServer [1] is used to access and query physically distributed and heterogeneous databases.

Integrated object networks are n-partite graphs, where the node types depend on the pre-defined object classes. Typically, relationships between molecular objects and the integration of data from several data sources lead to very complex networks. Here, we benefit from the application of object-oriented modelling concepts and databases at the structuring of integrated data. Applying pattern-based analysis at integrated networks, clusters of object interactions can be found out and can be stored as prepared network topologies in the system to be recalled laterly. They can be translated, e.g. into matrices, graphs and Petri-Nets, beeing the basic for network analysis, visualization and simulation.

The system (see figure) has been implemented using Java (programing language), CORBA (communication middleware) and ODMG databases (storage). The client applications "Database Builder"}, "Database Browser" and "Network Designer" are available under the URL: http://tunicata.techfak.uni-bielefeld.de/iiudb.

(*) This work is supported by the German Research Council (DFG)

[1] Freier, A. and Hofestädt, R. and Lange, M and Scholz, U. and Stephanik, A., BioDataServer: A SQL-based service for the online integration of life science data, In Silico Biology, Bioinformation Systems , Vol. 2, n. 5, 2001.
[2] Hofestädt, R. and Collado-Vides (eds.), J., Gene Regulation and Metabolism, Chapter "Information Fusion and Metabolic Network Control", The MIT Press, p.49--84, 2002.
[3] Freier, A. and Hofestädt, R. and Lange, M., IIUDB: An Object-Oriented System for Modelling, Integration and Analysis of Gene Controlled Metabolic Networks, Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'02) Novosibirsk, Russia July 14-20, ICG Novosibirsk, Vol. 2, p. 123--125, 2002.