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


CONCLUSIONS
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/.
Helt
Gregg A
GA
Genomancer Consulting, Healdsburg, CA 95448, USA. gregghelt@gmail.com
Nicol
John W
JW
Erwin
Ed
E
Blossom
Eric
E
Blanchard
Steven G
SG
Chervitz
Stephen A
SA
Harmon
Cyrus
C
Loraine
Ann E
AE
D003196:Computer Graphics; D016208:Databases, Factual; D023281:Genomics / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface
Genome Biol. 2005;6(1):301
15642109
Nat Biotechnol. 2009 Feb;27(2):153-5
19204697
Bioinformatics. 2009 Oct 15;25(20):2730-1
19654113
Science. 1993 Oct 22;262(5133):502-3
8211171
BMC Bioinformatics. 2002 Jul 30;3:19
12149135
Genome Res. 2003 Aug;13(8):1904-15
12869579
Genome Res. 1998 Mar;8(3):291-305
9521932
BMC Biol. 2005 Mar 22;3:7
15784138
Bioinformatics. 1999 Oct;15(10):837-46
10705436
Mol Biotechnol. 2000 Nov;16(3):221-32
11252807
Gene. 1995 Oct 3;163(2):GC1-16
7590260
BMC Bioinformatics. 2008 Nov 27;9:501
19038045
Bioinformatics. 2008 Sep 15;24(18):2096-7
18689808