Journal Articles

The Genoviz Software Development Kit: A Java toolkitfor building genomics visualization applications.

March 19, 2009

Helt GA, Nicol JW, Blossom E, Blanchard S, Chervitz SA, Harmon C, LoraineAE. The Genoviz Software Development Kit: A Java toolkitfor building genomics visualization applications. BMC Bioinformatics. 2009, 10:266.

Abstract

BACKGROUND:

Visualization software can expose previously undiscovered patterns in genomic data and advance biological science.

RESULTS:

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.

CONCLUSION:

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/.

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