Politics, Information Technology, and Genomics

Gathering cloud at XGen

If you are going to be at XGen next week and you are interested in cloud computing and its application to bioinformatics, be sure to stop and participate in the Cloud Computing in Bioinformatics discussion I will be "facilitating" on Wednesday morning (March 17). My talk is at 3:05 p.m. PT on Tuesday and I will be chairing the first session on Monday (if my plane is on time and the taxi is fast enough).... Full Post

Me, in podcast form

I recently did an interview in advance of my talk at the XGen Congress next month in San Diego. The interview is about 14 minutes and discusses our work at The Genome Center in general and more specifically the software and IT infrastructure we have created to enable the analysis of the massive amounts of sequence data we generate. The interview is available to download as part of the XGen Congress podcast series. Full Post

The Pac's out of the bag

Most of you have probably already seen this, but Pacific Biosciences announced the institutions that will be getting their first ten prototype instruments (Bio-IT World, GenomeWeb, MarketWatch). The Genome Center is among the institutions that will be getting one. It looks like PacBio will indeed be the first third generation sequencing company with instruments out in the wild. Don't get too excited though, it's probable that these third generation instruments will be a lot like... Full Post

Next-Generation Sequencing Informatics Update

I updated the Next-Generation Sequencing Informatics table a few weeks ago but forgot to mention it on the blog. The main update was the 50G configuration of the Illumina GA IIx. Also, the Sides & Associates blog linked to my table and referred to it as a "somewhat dated comparison of next-generation sequencing platforms." Just to clarify, this table represents average throughput for production systems; not vendor claims about throughput, not future vaporware (and Alejandro... Full Post

Puff piece

Why should one be skeptical of all the information touting the wonders of cloud computing? This older, in-depth piece by Gartner, Hype Cycle for Cloud Computing, 2009, lays out the reasons pretty well. But one need not spend that much time reading about it. You can simply read this much shorter piece by Jason Stowe: Is the Future Of High- Performance Computing For Life Sciences Cloudy? Reading that story, one can only get the impression... Full Post