Saturday, August 20, 2016

Where the bleep did my pores go??

Another afternoon spent this week in the lab, and another awful MinION run.  I figured that the last run was eminently beatable, given that I ended up with exactly one read aligning to my reference (though perversely, re-calling the data via Metrichor ended up with two reads in the pass folder -- one of which had zero bases in it -- I guess it is a passing null read).  But no, despite coming close to being botch-free on the routine lab stuff, dark clouds came early and the experiment yielded not a single usable read.

Wednesday, August 03, 2016

Sometimes It's More About the (1D) Journey

I will confess that I had a post planned in advance of which this post is but a faint echo. A grand scheme was going to yield a triumph worthy of brass bands.  But instead, it's barely kazoo territory, but sometimes even a small victory must be celebrated, if only in moderation.

Tuesday, July 19, 2016

Math Toys, Much Enjoyed!

Last week, I attended a free public talk at the Society for Industrial and Applied Mathematics (SIAM) here in Boston.  This is a wonderful public outreach concept which too few conferences sport.  The speaker, Tadashi Tokieda of University of Cambridge, illustrated a number of fascinating phenomena which can be demonstrated with simple toys or household objects.  Tokieda didn't lecture from a bunch of slides; most of the talk was in the form of live demonstrations -- and demonstrations made with overt glee!  There's a Storify of the entire meeting, in which mine and others of the Tokieda talk can be found.

Tuesday, June 21, 2016

Infinity's Sad RUD

Almost five years ago, I wrote of voluntarily leaving Infinity Pharmaceuticals.  Particularly due to the novelty (for me) of the voluntary part, at times I've wondered how long I would have stayed there.  Indeed, the offspring asked just that question just over a week ago. I do know now when I couldn't have stayed any longer, as to my great dismay Infinity announced last week it was discontinuing its Discovery operations due to a disappointing drug trial result.

Thursday, June 16, 2016

Writing Big

For the past few decades, since the early stirrings that led to the Human Genome Project, technology for reading DNA has gotten immense investment and attention.  Particularly noted, perhaps ad naseum, is the rapid decline in sequencing costs which outpaces Moore's Law for microprocessors.  The converse activity of writing DNA has generally played second fiddle, but these past few weeks have seen a flurry of headlines on that topic.

Friday, June 10, 2016

London Calling 2016: Further Thoughts

London Calling was two weeks ago, and I still haven't written anything beyond the write-up of Clive Brown's talk (note that many of the talks are now view-able via Oxford Nanopore's website).  I did finally make some headway on Storifying the tweets.  After several self-inflicted wounds (starting with failing to read my write-up of the previous experience of trying to post to Storify from the command line, but also from failing to record the details of that final critical command), I did succeed.  This time I decided to group the tweets into several broad categories -- with tweets potentially showing up in multiple categories, though these are a bit rough-and-ready and probably most folks will want to check multiple or all of the stories.  One major value I derive from this exercise is having them to refer back to, so I'll probably feel the pain of erratic characterization the most (though I also have the tweet database, so I could reslice these in new ways).  Anyway, the categories are: de novo Assembly, Bioinformatics and R9, Real Time and Read-Until, PromethION, Microbiomes, Clinical/Human (except Infectious Diseases), Infectious Disease and Biowarfare, Field Uses plus finally Library and Sample Prep (another one that failed initial upload; includes Zumbador and VolTRAX tweets).

There's supposed to be a final one encompassing everything that was left over, particularly general tweets about the conference.  Unfortunately, Storify balked at that one -- have to look again and perhaps break the set into at least two pieces.  (nope: worked with one)

Sunday, May 29, 2016

London Calling: Notes on Brownian Commotion

I'm behind on writing up London Calling.  I can partly blame a failing computer -- though rebooting it seems to have righted it for the moment.  A bigger challenge is that I had the luxury of staying in London thru the weekend, and have been trying to pack as much in of England as I can.  To really do justice to everything, I need to scan all the tweets  -- and that will take some time.

But I have dug into everything around Clive Brown's talk (kudos to NextGenSeek for Storifying that portion of the meeting's tweets!_ about the current and future state of the Oxford Nanopore platform, so I will focus on that, with a few side-trips on closely related topics. A few gaps on topics I previewed but didn't show up in the presentation were filled in with chats with Clive.  Plus, the indescribably huge advantage of actually going to a conference are the tidbits gleaned from late night chats over drinks (and no, I didn't ply anyone to get them to spill -- all was coughed up out of pure free will).  I'm going to roughly divide these by the announced timeframe: now, imminently, later this year, perhaps next year and unspecified.