I was at a get-together yesterday for bioinformatics folks associated with Third Rock Ventures companies at a local pub. The organizer, who I've known for a number of years, was introducing me with the pleasant "Keith writes a nice blog" -- but then the barb "but he hasn't posted in a while". Ouch! But it hurts because it's true; too many excuses to not write and far too many half-baked ideas and interviews that should be out (or worse, a nearly complete post). Since it is May, which in the U.S. is bookended by iconic racing events, I'd like to trot out an idea that has been idling for a while: PromethION Racing.
Monday, April 16, 2018
Back in October I covered the launch of Mission Bio's single cell platform, Tapestri. Tapestri is a microfluidic platform which encapsulates cells and sets of barcoded primers into droplets, lyses the cells within the droplets and executes PCR on the released DNA. Mission initially targeted hematologic cells, since they do not require disaggregation, and offered a standard panel of primes. Around the time of AGBT, Mission launched a custom panel option and took the time to sit down with me. Now with AACR, Mission has announced placing Tapestri at multiple major cancer centers: the NCI, Mt. Sinai, MD Anderson, Memorial Sloan Kettering, St. Jude's, UCSF, U Penn and Washington University.
Saturday, April 14, 2018
A movie opened this weekend which, by all prior evidence and new reviews, is unbelievably silly but destined to rake in the bucks. Rampage is very loosely - as if it could be another way - based on a video arcade game. The original game’s backstory had a mysterious ray transforming people into monsters, but the movie has changed that to CRISPR. So STAT had a piece which, to my great disappointment, gave the movie’s science a near pass in a piece featuring two writers chatting . . (Note: this post has mild spoilers, though if you've seen the trailers they give almost all of this away).
Wednesday, March 21, 2018
If you are in the sequencing business, you'd like to get things right. But sequencing is a form of measurement and measurement has error. No matter how diligent and committed you are, sometimes the data doesn't break your way. Mick Watson has a set of posts and a preprint illustrating quality issues in many deposited bacterial genomes. Some of those are bad luck and some of those are from complacency. Some errors radically affect biological interpretation and some don't. I'm going to detail here one of the worst cases of bad luck I've seen, where relatively small errors sat undetected for over a decade and triggered some published head scratching over their erroneous implications. So let's look at the rap sheet of this error.
Tuesday, March 06, 2018
I've written in the past about SeqLL, the company which purchased all of the hard assets from Helicos after the latter's demise. At the end of last year, CEO Elizabeth Reczek invited me to stop by for a visit and so I spent a morning having a frank discussion with Dr. Reczek and Director of Sales Lee Dalton and also was treated to a tour of their facilities.
Sunday, February 25, 2018
Due to the usual time conflicts, I've only watched bits-and-pieces of the Winter Olympics from South Korea. Which is unfortunate, as I do enjoy observing many of these events as so many combine grace, power and finesse. In the various timed events, the competitors can be seen tightly wound, ready to spring out at the crack of the start. Increasingly, that is how Oxford Nanopore's PromethION looks: a superb performer ready to bolt away.
Sunday, February 18, 2018
AGBT officially ended on Thursday night with a space-themed party, but I have a bunch of notes from interviews with company representatives and even a few notes from sessions. So be prepared for a string of further AGBT reports. This dispatch will have some overall thoughts as well as some notes on the possible return of AGBT to Marco Island next year. I also want to mention two good AGBT 2018 summaries, one from Dale Yuzuki and another from Decibio's Stephane Budel.