PolITiGenomics


Politics, Information Technology, and Genomics

How fast?

In a recent post, I spoke about the data format that will be used by the NCBI Short Read Archive (SRA), but storing the data is only part of the problem. You also need to get the data to the SRA. At the 1000 Genomes Steering Committee meeting last month, we got some idea of the number of massively parallel sequencers currently in use at the large sequencing centers around the world. There are about... Full Post


When stars align

If you are at all familiar with the massively parallel sequencing platforms, you know that the raw data, the images, look a lot like star field pictures. Once you process all these images, you get DNA sequences, called "reads". For these technologies, the reads are typically short, 30 to 50 bases, which presents difficulties when trying to align these reads back to a reference genome. For one, the shorter the sequence, the less unique it... Full Post


Bridging the gap

It is not everyday that you get to hear a Nobel laureate or the former director of the NIH speak. It is even less frequent that you get to hear someone who was both. For me, yesterday was such a day. Harold Varmus, MD, Nobel laureate, former director of NIH, and current president of Memorial Sloan-Kettering Cancer Center, gave The Julia Hudson Freund Memorial Lecture here at Washington University School of Medicine. His talk was... Full Post


454 XLR-HD

The next upgrade of the 454 FLX platform is called Titanium. The previous name gave a better indication of what the upgrade entails: XLR-HD which is short for eXtra Long Reads-High Density. The XLR is due to the run having twice the number of cycles so the average read length will increase from 250 to 400 bases (the average read length is not exactly double due to nucleotide flow order, mononucleotide runs, degraded signal as... Full Post


More candidate stances on technology issues

Similar to Ars Technica's list a couple weeks ago, PC Magazine is running a story about each presidential candidate's position on net neutrality, broadband availability, H-1B visas, intellectual property protection, and privacy. Full Post