Politics, Information Technology, and Genomics

UR so beautiful to me

Thanks to the hard work of a whole host of developers at The Genome Center, especially Scott Smith and Tony Brummett, UR, the class framework and object-relational mapping (ORM) layer we developed and use at The Genome Center, has been released on CPAN (actually, I am a little late announcing this, Scott has already uploaded version 0.3). UR is the foundation of the analysis pipelines I presented at the Biology of Genomes meeting at Cold... Full Post

The local press

Some media outlets take a little longer to recognize a story, even one in their own back yard. St. Louis Magazine, a local culture and dining monthly, has an article in the June 2009 issue about our whole-genome sequencing approach to studying AML entitled The Code Breakers. You can tell from the tenor of the interview, they're not exactly targeting a scientific audience (given their target audience this is neither surprising nor a bad thing).... Full Post

1000 Genomes phase change

The 1000 Genomes Project is transitioning from its pilot phase into the full project. Since 1000 Genomes is a mixture of data production centers and not a pure component, the phase change from pilot to full project is a continuum rather than a sharp transition. Some centers have already started sequencing of the full project while other centers are finishing up their pilot 3 (targeted, capture-based sequencing of 1000 genes) commitments, while some are doing... Full Post

Paul Flicek's a Mac

Paul may kill me for posting this, but I'll assume he allowed himself to be recorded and the video posted because he wanted people to see it. Enjoy. Full Post

Biology of Genomes Poster

Several people have asked for an electronic copy of my poster, Maximizing Utility of Genome Sequence Data (pdf) (posted on the Internet Archive). As is hopefully clear from the poster, in addition to high-throughput sequencing, we now have high-throughput sequence analysis. After listening to Lynda Chin's talk on the first evening of the conference, which described the arduous process of translating a single putative cancer driver mutation to its function in the cell, one can't... Full Post