Politics, Information Technology, and Genomics

UR explained

Tony Brummet from The Genome Center gave a presentation earlier this week at the St. Louis Perl Mongers meeting on UR. The kind folks at StL.pm have posted the videos for the geographically challenged to enjoy. Part 1 Part 2 You can find a PDF of the slide deck in the Files section of the StL.pm Google Group page. Full Post

Link pin, king pin, Ryskin

A bit off topic here, but a former professor of mine seems to be making a stir in the scientific community. Professor Gregory Ryskin has always been his own man; spending his time in the Soviet army reading the Feynman Lectures on Physics and not exactly drumming to the department chair's beat while I was at Northwestern. He also made a few enemies of students with his "no partial credit" policy: answers on the weekly... Full Post

Illumina cluster needs

There is an interesting thread over at the Solexa Google Group about the IT infrastructure needed to support an Illumina Genome Analyzer (GA). The discussion focuses mostly on the cluster and, to a lesser extent, the storage and network required to operate the instrument and generate sequence data (primary analysis). At The Genome Center, we use Platform LSF HPC as our batch scheduler and currently use lsgmake-gap to execute the GAPipeline (the Illumina primary analysis... Full Post

Learning opportunities

These links came to my attention this past weekend and I thought they might be of use to some of the readers here. First, you can access all course materials, even lectures, for the CS61A: Structure and Interpretation of Computer Programs course at UC Berkeley. The course comes highly recommended. Second, Melissa Kahney has aggregated links for a bunch of UNIX and GNU/Linux tutorials grouped by topic and target audience (beginner and expert). Full Post

Great Expectations

A colleague of mine at The Genome Center pointed me to this O'Reilly Radar blog post about the talks at OSCON 2009 that Allison Randal, one of the organizers, considers highlights. Very kindly, she mentions my talk, The Freedom to Cure Cancer. I have a rough outline of the talk clanging around in my head. Having it take shape on a slide deck is going to take some work (and a lot of time on... Full Post