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

被引：20

作者：

Helt, Gregg A. ^{[2
]}

Nicol, John W. ^{[1
]}

Erwin, Ed ^{[3
]}

Blossom, Eric

Blanchard, Steven G., Jr. ^{[1
]}

Chervitz, Stephen A. ^{[3
]}

Harmon, Cyrus ^{[4
]}

Loraine, Ann E. ^{[1
]}

机构：

[1] Univ N Carolina Charlotte, Dept Bioinformat & Genom, Kannapolis, NC 28082 USA

[2] Genomancer Consulting, Healdsburg, CA 95448 USA

[3] Affymetrix Inc, Santa Clara, CA 95051 USA

[4] Olema Pharmaceut Inc, San Francisco, CA 94107 USA

来源：

BMC BIOINFORMATICS | 2009年 / 10卷

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

FRAMEWORK;

D O I：

10.1186/1471-2105-10-266

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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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