BN++ - A Biological Information System
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doi:10.2390/biecoll-jib-2006-34
July 24, 2006
August 28, 2006
Jan Küntzer, Torsten Blum, Andreas Gerasch, Christina Backes, Andreas Hildebrandt, Michael Kaufmann, Oliver Kohlbacher and Hans-Peter Lenhof
Correspondence should be addressed to:
Jan Küntzer
Saarland University, Building E1.1, P.O. Box 151150, 66041 Saarbrücken, Germany
ed.bs-inu.fnioib@nullreztneuk
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 by biologists around the world. The sheer amount and heterogeneity of these data poses a major challenge: data integration and, based thereupon, the integrative analysis of these data. We present BN++, the biochemical network library, a powerful software package for integrating, analyzing, and visualizing biochemical data in the context of networks. BN++ is based on a comprehensive and extensible object model (BioCore), which has been implemented 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 a data warehouse. The Java-based viewer (BiNA) provides a powerful platform-independent visualization of the data using sophisticated graph layout algorithms. Currently, the data warehouse imports and integrates data from about a dozen important databases including, among others, sequence data, metabolic and regulatory networks, and protein interaction data. We illustrate the usefulness of BN++ with a few select example applications. BN++ is open source software available from our website at http://www.bnplusplus.org.