Thursday, February 25, 2016

Digging into the Illumina Lawsuit vs. Oxford Nanopore

Illumina's and University of Washington's filing of a patent lawsuit and related trade complaint against Oxford Nanopore made big news yesterday, with nice coverage from Mick Watson, GenomeWeb, Nature's Erika Check Hayden, Technology Reviews' Antonio Regalado,  BioIT World's Aaron Krol, and venture capitalist Vishal Gulati. Each of these covers the onetime partnership between the two companies and their acrimonious parting of ways.   Oxford Nanopore released a short and pithy response. Having failed to get an early jump on things, the ground is already well plowed.  So my sloth and inertia have forced me to take an unpleasant route I usually spend great effort avoiding: actually reading the complaints and the two key patents licensed from Jens Gundlach's group at University of Washington (US8673550 and US9170230 ) they cite.

Wednesday, February 24, 2016

Amplification-free, library-free sequencing? NanoString wants to be It

Perhaps the most unusual new technology to be unveiled at AGBT16 is NanoString's new approach to sequencing, which is in very early stages of development.  Called Hyb And Seq  the process is remarkable in being a purely hybridization-based single molecule method -- absolutely no enzymes are harmed during the operation of the system. That's remarkable -- the only enzyme-free (or nearly so) sequencing approaches to deliver serious amounts of data into Genbank are Maxam and Gilbert approaches (including Church's genomic sequencing and multiplex sequencing), and even those typically required restriction digestion of the target.

Saturday, February 20, 2016

AGBT16 Storify Completion & Rate Limits

AGBT16 ended a week ago, but for various reasons I'm just now catching up on my Storify project.  A vacation was in there but also some tool building.  As I was griping about the pains of organizing the tweets manually, Brian Krueger suggested what was already dawning on me (but it helps to be poked -- professional embarrassment is often a stronger motivator than pure annoyance) -- I needed to stop doing this purely manually.  So, off to deal with pulling in Tweets automatically and at least doing some organization programatically.

Friday, February 12, 2016

10X Launches Chromium (#agbt16)

10X Genomics launched their approach to obtaining long-range genomic information last year with a big financing and some exciting preliminary data at AGBT15.  Now they are back at AGBT16 with an upgraded instrument, improved biochemistry, new software and new applications, along with a trio of major co-marketing agreements and a splashy hire and a raft of both published and unpublished data from academic collaborators.

#AGBT16 Day 2: How is AGBT On Twitter Like Sequence Assembly?

I spent a bunch of time yesterday going through the Tweets from AGBT.  For me personally it is a useful exercise, plus I'll have it as a resource to go back to for future posts.  But the time and pain involved definitely had me sometimes questioning the wisdom of attempting this.

Wednesday, February 10, 2016

AGBT Begins (with bonus Storify Jeremiad)

Just finished my last Storify for tonight from AGBT16, and boy am I wondering how sustainable this will be.  The "problem", which is wonderful to have, is that the number of tweeters has grown substantially, and so there is a wealth of material to attempt to distill down. There's also the desire to make sure I don't further propagate the spam which sneakily re-tweets the occasional item. The other problem has been my tools

AGBT16 Preview (aka The Non-Attendee's Lament)

AGBT16  starts this today but I'm again not there. The usual complex set of personal constraints (or imagined ones) kept my hat out of the ring this year, and now I'm again torn between wanting to be there and why it would have been hard.  Easy would be leaving our most recent snow and ice storm and the general cold weather.  A bit harder is it is early in the school term, and back-to-school night is Thursday -- plus I spent last night chatting with a candidate for a local office (School Committee) at a low-key campaign event.  The big, and unforeseeable, challenge is that the other half of Starfleet's bioinformatics group is out on paternity leave, and while I'm proud of how much quotidian work I get done during conferences, it still isn't the same as being on full duty.

Tuesday, February 09, 2016

Why do we purify DNA the way we do?

An interesting conversation on Twitter on means for purifying DNA for PacBio and the risks of phenol-chloroform extractions restarted some pondering on the historical contingency of experimental techniques.  Or, as the title says, why do we (today) purify genomic DNA the way we do?