Next generation tools for genomic data generation,… [BMC Bioinformatics. 2010] – PubMed result

BMC Bioinformatics. 2010 Sep 9;11(1):455. [Epub ahead of print]

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

Nix DA, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ.



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 Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources.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,, and

PMID: 20828407 [PubMed – as supplied by publisher]

via Next generation tools for genomic data generation,… [BMC Bioinformatics. 2010] – PubMed result.

Save the economy, Fund Basic R&D

Great article in businessweek.  Look at the infrastructure that brought us most of the technology we use today – much of it was done by public-private parterships (e.g. Bell Labs, Xerox Parc, etc.).  If we want to recreate the jobs that have been lost during the recession, we need to put our faith back into the innovation that created the strong US economy – our intellectual leadership through scientific innovation.  Great article.