Genoviz Software Development Kit: Java tool kit for building genomics visualization applications

The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs) in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities.Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available at http://genoviz.sourceforge.net/ webcite.Since the beginning of the genomics era, numerous authors have warned against on-coming information overload, using metaphors that evoke natural disasters ("deluge," [1] "avalanche" [2], "tsunami" [3]) to emphasize how our capacity to generate data threatens to overwhelm our ability to deploy it in research. Finding ways to store and analyze vast amounts of data is not as difficult as it once was, thanks to improvements in database technologies, web services, and computer hardware, but developing graphical software that allows scientists to visualize, explore, and interact with novel and rapidly expanding data sets from genomics remains a challenging task.Flexible, highly-interactive visualization software has great value in genomics because it