title: BiNA: a visual analytics tool for biological network data.
abstract: Interactive visual analysis of biological high-throughput data in the context of the underlying networks is an essential task in modern biomedicine with applications ranging from metabolic engineering to personalized medicine. The complexity and heterogeneity of data sets require flexible software architectures for data analysis. Concise and easily readable graphical representation of data and interactive navigation of large data sets are essential in this context. We present BiNA--the Biological Network Analyzer--a flexible open-source software for analyzing and visualizing biological networks. Highly configurable visualization styles for regulatory and metabolic network data offer sophisticated drawings and intuitive navigation and exploration techniques using hierarchical graph concepts. The generic projection and analysis framework provides powerful functionalities for visual analyses of high-throughput omics data in the context of networks, in particular for the differential analysis and the analysis of time series data. A direct interface to an underlying data warehouse provides fast access to a wide range of semantically integrated biological network databases. A plugin system allows simple customization and integration of new analysis algorithms or visual representations. BiNA is available under the 3-clause BSD license at http://bina.unipax.info/.
authors.affiliation: Algorithmics, Department for Computer Science, University of Tübingen, Tübingen, Germany ; Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department for Computer Science, University of Tübingen, Tübingen, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Gerasch
authors.affiliation: Algorithmics, Department for Computer Science, University of Tübingen, Tübingen, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Faber
authors.affiliation: Roche Diagnostics GmbH, Pharma Research and Early Development Informatics, Penzberg, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Küntzer
authors.affiliation: Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department for Computer Science, University of Tübingen, Tübingen, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Niermann
authors.affiliation: Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department for Computer Science, University of Tübingen, Tübingen, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
authors.affiliation: Center for Bioinformatics, Saarland University, Saarbrücken, Germany.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Lenhof
authors.affiliation: Algorithmics, Department for Computer Science, University of Tübingen, Tübingen, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Kaufmann
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D057225:Data Mining / Q000379:methods*; D003628:Database Management Systems; D016208:Databases, Factual; D053263:Gene Regulatory Networks; D006801:Humans; D053858:Metabolic Networks and Pathways; D025941:Protein Interaction Mapping