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?

Thursday, January 28, 2016

First on an occasional series on high school biology: Complexes

TNG has biology this term, so I will be (at erratic intervals, of course) sometimes venturing my thoughts on the teaching of that specific subject.  I think I never quite got around to venting the last time he had a biology unit, back in middle school, which among its sins was still teaching the seven kingdoms system of classification, which for the love of Woese is absurd.

Friday, January 22, 2016

Does any analytical program really care about the order of paired end files?

I was recently experimenting with C. Titus Brown and company's khmer package and hit an interesting little snag.  First, I had my usual problems with installing a Python-based program, which were solved by the totally counter-intuitive absurdity of actually following the installation directions precisely. Armageddon is certainly near if random shortcuts and assumptions can't be relied on to get the job done.  But once I had it working for a simple test case, I crazily tried to build something -- and that's when a new, maddening bug cropped up.

Monday, January 18, 2016

Illumina's MiniSeq Giveaway

This morning, Illumina announced a Scientific Challenge program as part of the launch of the MiniSeq sequencing instrument.  Three prizes will be given away, with 3 sequencing runs on MiniSeq as 3rd prize and a MiniSeq plus reagents for 3 runs as second prize, and a MiniSeq plus reagents for 3 runs plus a Mini Cooper automobile as the grand prize. Entrants in the contest will submit a proposal for how to they plan to use the instrument (but not the car; if you support future reagent purchases by being an Uber driver, that's your business). There will also be a set of iPad mini giveaways based on recommending colleagues to enter the contest on social media; if your recommendation results in an entry, then you are entered in the iPad giveaway.

Tuesday, January 12, 2016

Illumina's Unveils Firefly

Illumina third big announcement around JPM is to unveil Project Firefly, a semiconductor sequencer which will use existing SBS library preparation and a derivative of SBS chemistry.   Slotted with a price point ($30K), physical size (small pizza box ish?) and data yield (4M reads, 1Gbp data)  below the just announced MiniSeq , Firefly would be two small boxes which could stack: one for library preparation and one to run single channel sequencing.  The flowcell would use ordered arrays, layered atop the semiconductor sensors.  Launch is proposed for the second half of 2017.


Okay, third (and last) post for tonight.  Time for the victory lap -- and a reminder of the limits of educated guessing.  On Sunday I threw out a prediction of a hypothetical Illumina MiniSeq based on ordered arrays, NextSeq chemistry and optics, but with only one optical unit and a price point of about $50K -- and today Illumina announced precisely that.

Monday, January 11, 2016

Grail will change oncology & society, but how?

Second big genomics news this weekend around the JP Morgan is that Illumina is spinning out a new company called Grail, backed also by Jeff Bezos, Bill Gates and some VCs, to pursue mass cancer screening via liquid biopsies.  Given that cancer is most treatable when caught early, it's an exciting idea.  But, the devil as always is in the details, and they could be quite diabolical.

Affymetrix Assimilated

With JP Morgan Conference starting, there's lots of big news in the genomics world, and for 2016 I'm throwing out my previous internal policy of one post per day; if the news warrants multiple, then write multiply! Plus, too often in the past I've jammed topics together, and if nothing else it makes it hard for me to find my own posts on a topic! The first big news this weekend is the announcement that Affymetrix has been snared in a $1.6B tractor beam from Thermo Fisher.