Saturday, February 28, 2015

What's Been Cooking for Ion At AGBT15

Rounding out my remote coverage of platform news from AGBT, the Ion Torrent team also lent me some of their time (and at risk of sounding obsequious, I do greatly appreciate this -- vendors have almost no down time at these events) to touch on some of the topics I I wrote about in my Ion history and speculation piece.

Friday, February 27, 2015

10X Reveals Its Facets

Perhaps the heavily anticipated launch at AGBT this year is the library prep instrument for 10X Genomics.  This Bay Area startup made a huge splash at the beginning of the year by announcing a monster ($55.5M) financing.  A member of my professional network had been part of the early team and had given me very minimal hints at last year's AGBT, so I've been eagerly awaiting details for a long time. Several members of 10X's team were kind enough to chat with me by phone yesterday with the proviso that I hold off on launching this piece after their talk today at the conference (interestingly, I had crossed paths with all of them in some previous setting).  Also, they sent me some promotional materials and permitted me to post some clips from them. Now, the GemCode system is officially launched, with orders being taken now and devices planned to be delivered in early Q2.

Wednesday, February 25, 2015

Illumina Launches NeoPrep (#agbt15)

The 2015 AGBT conference started out today.  A few hardware makers have let me chat by phone with members of their team, since they're there and I'm not.  Tonight's dispatch is from a chat with Illumina focused on their now launched NeoPrep library preparation instrument

Sunday, February 22, 2015

Can Ion Torrent Buzz Again?

In my AGBT 2015 Preview / Speculation at one point had a tightly packed (and overly long) paragraph on Ion Torrent, but I realized that this was a symptom of trying to to cram too much in too little a space -- plus I really had a lot more thoughts worth unpacking.  So here's a long form look at Ion Torrent -- with plenty of references to past AGBTs to make writing this now apropos.  One advance bit of excuse making: the historical background that follows is not intended to be a comprehensive history of Ion Torrent technology, but more of an impressionistic sketch (but as always, my worst excesses and omissions are fair game for comments!).

Saturday, February 21, 2015

#AGBT2015 Preview

The annual genomics party on Gulf of Mexico beaches named AGBT runs next week, and already there have been some speculations flying.  I'd better dash something off before I'm any later to the preshow -- or more importantly before I get contaminated with embargoed information.

Wednesday, February 11, 2015

The MBTA Must Embrace Data!

As you may have heard, we’ve had a bit of snow in the Boston area recently.  Two storms, one the beginning of last week and one which just ended yesterday, each dumped close to a meter of snow in the area.  The two storms each had different profiles: last week’s storm featured rapid snowfall and furious winds, with the snow falling over a 24-36 hour period.  The more recent storm started on Friday afternoon, ended on Tuesday morning, with a steady fall of lazy snowflakes.  Last week a hare, this week a tortoise.  But both weeks, a paralyzed Boston from a transportation standpoint, with the MBTA mass transit system performing dismally.

Unfortunately, the main response to that failure has been a lot of political theater. GM Beverly Scott gave a press conference yesterdaythat featured the usual refrain: the system features antiquated equipment, our crews are working hard, nobody could deal with this.  In other words, a string of unquantifiable and unactionable clich├ęs.  There's already an unhelpful murmur in the press that Scott might be fired, which would seem little fix but mostly fodder for more column inches of newspaper opinion (such as this and this)

Saturday, February 07, 2015

How not to write a sequence assembly comparison paper

Lex Nederbragt flagged, via Twitter, a preprint on the F1000 site with a questionable table comparing sequencing systems.  Alas, once I looked at the paper I've gotten myself in a state where only writing up its numerous deficiencies will free my mind of it.  I've even volunteered to F1000 to review the paper, but I haven't heard anything and so I will use this space.  I'm afraid this paper fall into the small category of manuscripts that I would recommend rejection.

The preprint is titled "Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly".  Alas, the paper doesn't attempt to deliver anything of the scope promised by that, and the abstract isn't much better.  Most papers have a certain amount of preamble and then deliver some new finding; the preamble to the paper is overlong and badly executed, and the work in the paper is far too minimal and also badly executed.