Introduction

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

Publications

  1. Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.
    Cite this
    Helt GA, Nicol JW, Erwin E, Blossom E, Blanchard SG Jr, Chervitz SA, Harmon C, Loraine AE, 2009-08-01 - BMC bioinformatics

Credits

  1. Gregg A Helt
    Developer

    Genomancer Consulting, Healdsburg

  2. John W Nicol
    Developer

  3. Ed Erwin
    Developer

  4. Eric Blossom
    Developer

  5. Steven G Blanchard
    Developer

  6. Stephen A Chervitz
    Developer

  7. Cyrus Harmon
    Developer

  8. Ann E Loraine
    Investigator

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Summary
AccessionBT003498
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAnn E Loraine