Information and simulation systems for the analysis of gene regulation and metabolic pathways (Preface)

The internet is developing into the most powerful medium for information retrieval. This factis consequently reflected in molecular biology. With the automated high throughputexperimental technologies that have been developed in the last years, a large number ofresearch projects are currently producing an exponentially increasing amount of data. Onlythe Human Genome Project by itself produces 3*109 base pairs and mapping data. In order totake advantage of the potential of valuable databases it has to be considered that there is arequirement for standardized, integrative and homogeneous access to data from a wide rangeof sources using powerful query languages e.g. SQL. Thus, the integration of databases andthe offering of a declarative query language can help scientists to detect new information andcoherence to find correlations across the spectrum from genomics via proteomics up to drugdesign.The idea of a mediator based database integration approach, called BioDataServer (BDS), hasresulted in an architecture, which is realized as a client-server system. Where the BDS is theserver and any molecular biology application, including database import modules, could actas clients. The homogeneous database access is realized by specific adapters. The BDS areable to process read-only SQL queries. On this basis a JDBC with XML capabilities and anODBC driver have been implemented. The attachable software ranges from simple analysistools via various molecular information systems up to complete frameworks for complexproblems like simulations. Further information, applications, demos and drivers are availableusing the URL http://integration.genophen.de. Selected ReferencesFreier, A. et al, MARGBench An Approach for Integration, Modeling and Animation ofMetabolic Networks, in Proceedings of the German Conference on Bioinformatics (GCB ‘99),Hannover, Germany, 1999, pp. 190-194.Hofestaedt, R. et al., Information Processing for the Analysis of Metabolic Pathways andInborn Errors, BioSystems, 1998, vol. 47, pp. 91-102.Köhler, J. et al., Logical and Semantic Database Integration, in BIBE 2000: IEEEInternational Symposium on Bio-Informatic & Biomedical Engineering, Washington, D.C.,U.S.A.: IEEE Computer Society, 2000. pp. 77-80. LinksBDS online Demos (phpMetatool, XML Browser, BioDataServer Demo Applet):http://integration.genophen.de/