Tuesday, February 1, 2011

Sneak Peak: AGBT and the Next Gen Software Challenge

The Advances in Genome Biology and Technology meeting begins Thursday (2/3) morning with pre-conference workshops on Wed.  I will be there representing Geospiza and presenting a poster entitled, "The Next Gen Software Challenge: Integrating Diverse Assay-Seq and Validation Systems" (abstract below)

In addition to great science and technology AGBT has a large number of tweeting participants including @finchtalk. You can follow along using the #AGBT and (or) #AGBT2011.  

By the end of 2011 we will know the DNA sequences for 30,000 human genomes. Understanding how the variation between these genomes affects phenotype at a molecular level, requires that future research projects integrate genome sequences with data from multiple ultra-high throughput assays obtained from large sample populations. Further insights are gained when these data are combined with additional information from external databases and data resources.

Geospiza is meeting the above challenges with its GeneSifter® platform and underlying open-source HDF5 and BioHDF technologies. Our approach centralizes and structures data in a scalable way so that features can be queried across many samples and between different assays to quickly add context to genome sequences as they are collected. Unlike approaches that rely on collections of flat files, specialized software tool kits, isolated genome-browsers, and independent statistical tool environments, GeneSifter integrates common components into a system that provides researchers with a rich, easy to use, environment to explore their data and develop clinical insights.

By: Todd Smith (1), N. Eric Olson (1), Rebecca Laborde (3), Christopher E Mason (2), David Smith (3):  (1) Geospiza, Inc., Seattle WA. (2) Weil Cornell Medical College, NY NY.(3) Mayo Clinic, Rochester MN.

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