Abstract
Recent years have seen an explosive growth in the amount of biochemical data available.Numerous databases have been established and are being used as an essential resource bybiologists around the world. The sheer amount and heterogeneity of these data poses amajor challenge: data integration and, based thereupon, the integrative analysis of thesedata. We present BN++, the biochemical network library, a powerful software packagefor integrating, analyzing, and visualizing biochemical data in the context of networks.BN++ is based on a comprehensive and extensible object model (BioCore), which has beenimplemented as a C++ framework, a Java class library, and a relational database. The C++framework is used to efficiently import, integrate, and analyze the data, which is stored in adata warehouse. The Java-based viewer (BiNA) provides a powerful platform-independentvisualization of the data using sophisticated graph layout algorithms. Currently, the datawarehouse imports and integrates data from about a dozen important databases including,among others, sequence data, metabolic and regulatory networks, and protein interactiondata. We illustrate the usefulness of BN++ with a few select example applications.