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

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 Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources.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.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.The post-genomic era holds many promises for addressing fundamental questions regarding biology and improving patient outcome through personalized medicine. It also 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. The bottleneck is less the cost and difficulty of generating the data but, more so, efficiently managing, analyzing, and distributing it. Here, we present three, open source, platform independent, software tools that we have developed to address each of th