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Open Access Highly Accessed Software

Next generation tools for genomic data generation, distribution, and visualization

David A Nix14*, Tonya L Di Sera2, Brian K Dalley3, Brett A Milash4, Robert M Cundick2, Kevin S Quinn2 and Samir J Courdy2*

Author Affiliations

1 Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA

2 Research Informatics, Huntsman Cancer Institute, Salt Lake City, USA

3 Microarray/Next Generation Sequencing Shared Resource, Huntsman Cancer Institute, Salt Lake City, USA

4 Bioinformatics Shared Resource, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA

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BMC Bioinformatics 2010, 11:455  doi:10.1186/1471-2105-11-455

Published: 9 September 2010

Abstract

Background

With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data.

Results

Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser.

Conclusions

These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/ webcite, http://sourceforge.net/projects/genoviz/ webcite, and http://sourceforge.net/projects/useq webcite.