I will confess that when our first MinION burn-in data for lambda came in & I threw a few aligners at it (after first getting my data extractor in Julia shaken out), I was disappointed at the results. Very few 2D reads, very few aligned reads and the alignments all short. At this point, I sat back to wait to see what others had experienced and to think of additional bioinformatics approaches. It never occurred to me to dash off a glorified blog post and submit it to a journal.
Tuesday, September 09, 2014
Friday, September 05, 2014
A huge event in the genomics community this summer has been the Oxford Nanopore MinION Access Program (MAP), which has enabled a sizable but select group of researchers to try out ONT's novel nanopore-based sequencing technology. While results and rumors have periodically drifted out over the summer, this week saw three disclosures, one of which resulted in fireworks and action
Monday, June 30, 2014
As I mentioned recently, I've been exploring how I might use the emerging Julia language to solve problems. While that requires a large amount of mental work, I see some potential gains, both in having more readable code than Perl as well as to potentially leverage a lot of high-level concepts for parallel execution that are built into the language. But beyond the challenge of elderly canine pedagogy that I present, there is the issue that the BioJulia library is quite embryonic, with serious consideration of treating much of the existing code base as a first draft (or, that is the impression I get from skimming the Google group). So I'm going to try to pitch in, despite my multiple handicaps.
Tuesday, June 24, 2014
I don't read a lot of books aimed at the MBA crowd, but one set I have liked, and sometimes cite here, are Clayton Christensen's on inovation and disruption. As you may have heard, a recent article in the New Yorker by Jill Lepore took a gimlet-eye view to the whole concept and raised serious questions about Christensen's methods. This was then summarized by another author in Slate and since then Christensen has responded in part via a Business Week interview. He's also scheduled to be interviewed on PBS this weekend, so likely there will be further developments. Indeed, after sketching this out on the commute home I discovered a Financial Times article whose tone is very similar to what I have written below.
Tuesday, June 03, 2014
As I've remarked before, I've done significant coding in a large number of languages over the last 35-or-so years. I don't consider myself a computer language savant; I've known folks who can pick up new languages quickly and switch between them facilely, but for me it is more difficult. I haven't tried learning a new language in perhaps 5 years, but this week I backed into one
Wednesday, February 26, 2014
One of the most electrifying talks at AGBT this year was given by Joe DeRisi of UCSF, who gave a brief intro on the difficulty of diagnosing the root cause of encephalitis (as it can be autoimmune, viral, protozoal, bacterial and probably a few other causes) and then ran down a gripping case history which seemed straight out of House.
Monday, February 24, 2014
The sun set during AGBT 2014 for a final time over a week ago. The posters have long been down, and perhaps the liver enzyme levels of the attendees are now down to normal as well. This year’s conference underscored a possibility that was suggested last year: that the era of the poorly connected, low quality draft genome is headed for the sunset as well