Politics, Information Technology, and Genomics

Platform independent

When Java first hit the software development scene, the mantra was "write once, run anywhere". Well, Java, or more precisely the way computer science departments use Java, has received some criticism recently, but it was not related to that mantra, despite the fact the mantra's goal is rarely achieved. While Java runs on the Java Virtual Machine (JVM) which is, in theory, platform independent, Java does not prevent developers from hard-coding platform-specific assumptions in their... Full Post

454 Informatics

I recently received this request. We've taken on 454 sequencing and would like information about the amount and type of bioinformatics support needed to help investigators with their data. Our goal is to outfit our bioinformatics analysis core with talent sufficient to align, assemble and annotate pathogen genomes and large sections of genomes, as well as targeted sequencing following up on association studies. In truth, I have recently received a lot of requests like this.... Full Post

Post-debate coverage

I watched the Democratic debate in Las Vegas this evening. It was a good debate after they got down to real issues and policy matters. I think all the candidates did well, each had their good moments, and each had times they stumbled a bit. I was pleasantly surprised that when asked what their weakest point was, Barack Obama actually gave a real answer, i.e., not the standard "I guess I care too much about... Full Post

You've got a plumbing problem

Last week I attended the TCGA Data Portal Use Case Workshop. TCGA stands for The Cancer Genome Atlas and is an ambitious project to more fully characterize and understand the molecular, i.e., DNA-level, mechanisms at work in cancer. While the end goal is to gain a rich understanding of all types of cancer, TCGA is a three-year pilot program investigating three types of cancer (brain, ovarian, and lung) and testing whether its approach to study... Full Post

Martin Luther King, Jr.

Today is the Rev. Dr. Martin Luther King, Jr.'s birthday. Martin Luther King Jr. Day will be observed this coming Monday, January 21, 2008. It seems he is back in the news lately due to the rhetoric around the Democratic presidential nominee campaigns. Is that how he would want to be remembered? Here is a letter titled "A Call for Unity" that several Alabama clergy published in a local Birmingham, Alabama newspaper on April 12,... Full Post