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

TitleGenoviz Software Development Kit: Java tool kit for building genomics visualization applications.
Publication TypeJournal Article
Year of Publication2009
AuthorsHelt GA, Nicol JW, Erwin E, Blossom E, Blanchard SG, Chervitz SA, Harmon C, Loraine AE
JournalBMC Bioinformatics
Volume10
Pagination266
Date Published2009 Aug 25
ISSN1471-2105
KeywordsComputer Graphics, Databases, Factual, Genomics, Image Interpretation, Computer-Assisted, Information Storage and Retrieval, Programming Languages, Software, User-Computer Interface
Abstract

<p><b>BACKGROUND: </b>Visualization software can expose previously undiscovered patterns in genomic data and advance biological science.</p><p><b>RESULTS: </b>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.</p><p><b>CONCLUSION: </b>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/.</p>

DOI10.1186/1471-2105-10-266
Alternate JournalBMC Bioinformatics
PubMed ID19706180
PubMed Central IDPMC2746221
Grant ListR01 HG003040 / HG / NHGRI NIH HHS / United States
R01HG003040-02S1 / HG / NHGRI NIH HHS / United States