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

David A Nix,Brian K Dalley,Robert M Cundick,Tonya L Di Sera,Kevin S Quinn,Brett A Milash,Samir J Courdy

doi:10.1186/1471-2105-11-455

David A Nix, Brian K Dalley + Show 5 more

Open Access

https://doi.org/10.1186/1471-2105-11-455

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Journal: BMC Bioinformatics	Publication Date: Sep 9, 2010
Citations: 58	License type: CC BY 2.0

Affiliation: Huntsman Cancer Institute, University of Utah

Abstract

BackgroundWith 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.ResultsHere 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 Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources.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.ConclusionsThese 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/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq.

Highlights

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
It presents several unique challenges that need to be addressed to maximize the effectiveness of using genomic data in the laboratory and clinic
One key issue is the exponential growth in the number, size, and complexity of datasets generated from genomic experiments

Summary

Results

We present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data These include a 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. 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

Background