Thursday, October 01, 2015

PacBio Sequel: Smaller Box, Bigger Bang

Boy, am I regretting taking a vacation from online due to being engrossed in A Canticle for Leibowitz.  Between last night and this morning, my neglect of my Twitter feed meant a colleague tipped me to the new PacBio machine with "what's this Sequel I keep hearing about from PacBio".  So a lot of folks had a huge jump and covered it pretty well, including Keith Bradnam, Mick Watson, and James Hadfield.  Long rumored, the new instrument costs about half as much (but that's still $350K), takes up much less floor space (and doesn't need any reinforced floors) yet the new flowcells deliver about 6 7 times as many reads than the older ones.  WOW!

Thursday, September 24, 2015

Farewell Nabsys

A bit over a week ago brought news that mapping instrument hopeful Nabsys had ceased operations.  As a veteran of one failed biotech, I have a lot of sympathy for the team there. Plus, I knew a bunch of folks at the Providence RI firm.  Nabsys's signle molecule mapping technology was a wonder -- what single molecule technology isn't? Already stories are emerging of a disgruntled founder who wants to buy up the intellectual property and give it another go. It is easy to admire that stick-to-it spirit; it's a lot harder to find a rational reason to believe that such a revival will be any more successful.

Thursday, September 17, 2015

How Do You Differentiate Archea and Bacteria in the First Week of High School Biology???

I have a long standing interest in biology education -- I seriously considered it as at least a career to explore -- but now I really have skin in the game.  TNG just executed a schedule move that will defer his biology this year to the second half of the term, but I also have a niece who is taking AP Biology at her STEM high school.  Even in his short time in biology class, TNG has succeeded in asking for homework help that has me scratching my head.

Wednesday, September 09, 2015

Freely & Unrepentantly Confessing to Heresy

Keith Bradnam reported a huge influx of traffic for a recent post -- not surprising, since he labeled it NSFW (Not Safe For WorK).  And yes, despite my skepticism that it would be truly offensive, I'll confess I checked it with phone, not my work laptop.

Tuesday, September 01, 2015

Ion's S5

The Ion Torrent team rolled out a new sequencer line this morning, the S5.  The S5, whose impending release had been tipped on the internet by the leak of a manual, arrives in two models, the standard and the XL, which differ only by on-board computing power and not sequencing metrics.   As has been the trend, Ion's focus is entirely on focused sequencing, and the new lineup emphasizes making targeted sequencing with AmpliSeq and other approaches fast and simple.

Wednesday, August 26, 2015

The Road to Hell is Paved with Bioinformatics Formats

If you really want to raise a bioinformaticist's blood pressure, loudly declare your new tool generates output in brand new data formats.  This leads to the frequent observation that a large fraction of bioinformatics work is simply converting formats. It is probably consensus that the field is awash in too many formats, though it is equally clear that we can't agree on which should survive.  Between some recent news and a Twitter thread on the subject that erupted last night, there was a bunch of fodder for me to collect in a Storify -- and to lay out my own idiosyncratic views.

Monday, August 24, 2015

Do Helix's Numbers Work?

A number of efforts in the consumer genomics space have been attempted in the past, with 23andMe appearing to make limited headway and Knome not much at all.  I haven't been able to get any investment interest in my own concept, though perhaps that's because it was tongue-in-cheek (or tongue held out while panting).  Last week brought a big splash, with a new company Helix launching with $100M and three major players as backers: Illumina, LabCorp and the Mayo Clinic