Back in January, at the end of my post on Illumina's new machine lineup I speculated whether Illumina might see a niche for a lower cost, lower throughput sequencing system that would slot below the MiSeq in their lineup. Such an instrument, I posited, might go after applications in biosurveilance and diagnostics where relatively small amounts of data are needed quickly. I speculated that perhaps a smaller instrument with less expensive optics could compete in this arena, which is heating up due to Oxford Nanopore and the growing acceptance of DNA-based diagnostics. As luck would have it, a few days later Molly He, Mostafa Ronaghi and colleagues at Illumina actually published a proof-of-concept paper for just such an instrument. Unlike many sequencing technology PoC papers, this one demonstrates feasibility of reading actual templates (phiX rides again!).
Tuesday, May 26, 2015
Wednesday, May 20, 2015
The second, and final, day of Oxford Nanopore's London Calling conference concluded last Friday -- and I'm behind on writing it up. Some of that was due to travel (and the wrong power supply going on the trip) and post-trip exhaustion, but failing to finish this last night was pure slacking. That route was shut down when one reader asked when I'd get things done. Anyway, I again organized the activity into a storify story as I did for the first day of the conference. I'm going to go into less detail on individual presentations below and instead engage in the vice of far-ranging speculation.
Friday, May 15, 2015
Wednesday, May 13, 2015
Oxford Nanopore's London Calling confab starts up in a matter of hours. Alas, several issues scotched my plans to attend (not only does it promise to be an exciting conference, but I simply love exploring London on foot). It is worth emphasizing that the MinION devices and consumbables have been out in the wild for not quite 11 months at this time. In that time, Oxford has dealt with a wide variety of technical and logistical headaches. While performance is still variable, many MAP participants are forging forward and the available tools for nanopore data continue to grow. London Calling will likely bring a burst of new announcements; Oxford's Clive Brown has been giving talks recently but has promised that exciting stuff has been reserved for the confab. Below is a set of semi-informed speculations calling out likely happenings, mostly based on Clive's recent presentations and tweets.
Pacific Biosciences had a string of announcements around its earnings release last week. Of particular interest is a collaboration with RainDance to develop a new sample preparation system for generating long synthetic reads from minuscule inputs. If some of that sounds familiar, the loose outline in the press release suggests an approach similar to that of 10X. But is this proposed system arriving too late to the party?
Monday, April 27, 2015
As mentioned previously, by wonderful luck I now have regular contact with Ash from the Curious Wavefunction, and he has stimulated a new burst of scientific history interest in me. I've ripped through a bunch of scientific memoirs -- by Crick, Djerassi and Dyson -- and have learned how to summon the biographies of Wilkins and Chargaff, as well as trying to dive again into The Eighth Day of Creation. One topic I keep stumbling across is an interesting little bit of genetic history called the RNA Tie Club, which is a story worth re-telling and re-examining
Monday, April 13, 2015
I'm generally a big fan of Wikipedia and use it often for background research. I've gotten more active this year in editing it, particularly around biographies of scientists. For example, this year I've made major additions or edits to the entries for Walter Gilbert and Arthur Pardee and the , created entries for Martinas Ycas, Benno Müller-Hill, Monica Riley and Helen Donis-Keller. I also stumbled my way into a campaign of major revisions to the entry on Marie Antoinette, getting sometimes into a revision war with one other editor (which we resolved with a truce). Along the way I've gotten almost adept at writing Wikipedia references and discovered a bizarre recurrent vandalism of Wally's page in which the vandal changes his name and personal details. Recently, I've discovered a whole category of flawed entries: those on companies in the biotechnology industry.
Tuesday, March 31, 2015
Through a happy series of professional events, I now get to have lunch very regularly with the author of the excellent blog The Curious Wavefunction. If you haven't visited there, Ash not only delves into chemistry but the history of science. In a most friendly way, he dropped a challenge on my Twitter-step that represents a long procrastinated blogging project, so I really couldn't turn it down. And that challenge is: what has been the value of cancer genomics. Is it, as he asked, a very expensive exercise in looking for keys under the lamppost, or something far more valuable?