Politics, Information Technology, and Genomics

Darwin must die, long live Darwin

A couple of days ago, Carl Safina had an essay in The New York Times entitled Darwinism Must Die So That Evolution May Live that discusses the cult of personality that has grown up around Darwin and how it is hurting the acceptance of the theory of evolution. Much of what he says about how little of what we now know about evolution actually originated with Darwin is correct, but the case for killing Darwin... Full Post

The scale up

It was announced this morning that we will be getting 21 more Illumina GA2 instruments, bringing our total to 35 at The Genome Center. No doubt it will be a great challenge and a great opportunity. Here is a graph I presented in my talk last night showing the acceleration in informatics staff, CPU, storage, and sequence generation (the absolute values of each line have been scaled to the same range since all the data... Full Post


I forgot to mention in my previous post about AGBT 2009 that Niel Das from our LIMS group will be presenting a poster about our NCBI SRA data submission pipeline and infrastructure. For all you struggling with that impenetrable XML specification, here's your chance to ask an expert. Full Post

File formats aplenty

In a previous post on the 1000 Genomes Project, David Sexton from the Center for Human Genetics Research at Vanderbilt University asked about the new file formats for alignments, assembly, and genotype data. The alignment and mapping format is called Sequence Alignment/Map or SAM. The specification is available as a PDF and there is also a C library (API) available for working with SAM files. You can download the C source code and tools for... Full Post

A cry for help

This morning I got this message in an email from the Director of the St. Louis Crisis Nursery. Dear Friends, As the economy continues to spiral downward, families throughout our area are struggling every day to care for their little girls and boys. They must choose between buying food or paying rent. They must decide if they can afford diapers this week or if they will need the money to keep the lights on. I'd... Full Post