Monday, August 31, 2020

Self-Assessing My Python

I've been programming 90+% in Python now for over a year and a half -- when I joined the Strain Factory I vowed to finally make the break from Perl.  Partly this was disgust with so often finding libraries I wanted to be missing or broken, and partly it was recognizing that the Factory is primarily a Python shop and I would have the most impact if I worked in the lingua franca. I was first exposed to Python back at Codon Devices, but there was a strong C# faction there and I fell in love with that language, so my primary dabbling in Python was learning enough to glue the key Python code into my C# with IronPython.  I strongly considered changing over at the start of Warp Drive, but gave it too weak a try and quickly started churning out Perl.  I still use that language for basic level text munging, but have avoided writing nearly anything that occupies more than one screen.

Friday, July 24, 2020

Two Pandemic-Related Programming Problems

I will offer here two bioinformatics programming problems which I think are interesting, useful and should be approachable by an advanced undergraduate.  For a variety of reasons I've been thinking a lot of about skill levels and how to assess them.  One key reason is we have two open slots in our group, so I'm plowing through CVs and engaging in the usual hiring funnel struggle -- how do you winnow CVs to phone screens and then down to interviews? We also thought we might, but now won't, bring on a one year intern.  But I'm also trying to take a look at my own skill set with a critical eye.  Plus I maintain a Quora addiction, and you see there people looking for ways to prove their computational biology chops.

Monday, June 29, 2020

Virtual London Calling, Veritably Late, Part II: Platform Development

Last time, I covered Oxford Nanopore LamPORE COVID-19 detection scheme.  London Calling was over a week ago, so the chance to scribble before its all old news is rapidly shrinking.  As noted yesterday, Clive Brown didn't speak here but instead will broadcast at some future date; it was left to his top technical lieutenants to cover the developments in the platform which have happened since the Community Meeting in New York back in early December.  I've tried to hit the highlights here, but don't claim to be comprehensive.

Wednesday, June 24, 2020

Virtual London Calling, Veritably Late Copy: Part I, LamPORE

London Calling was last week, held online due to the pandemic.  My plans to attend in person were one of a myriad of travel arrangements upended by the calamity, though that is utterly trivial in comparison to the tragedy of so many lost lives, damaged survivors and economic ruin.  Attending remotely also made it harder to ignore my work duties, which are at a crescendo (well, not really: it's been this intense for months).  But all the talks are available online, so I have stolen some time to review the Oxford Nanopore technology announcements.  There wasn't a Clive Brown talk; apparently he will deliver a broadcast later this summer to tease us with more crazy ideas emerging from the ONT Skunk Works.

Friday, May 29, 2020

Roche Expands Sequencing Nanopore Presence by Acquiring Stratos Genomics

Ugh.  I let the month of April slip away without writing and now have almost let May do the same.  But some leftover euphoria from a huge experimental breakthrough on our current diagnostics project at the Gene Factory plus the feeling I shouldn't let news tied into an earlier post slip off, and here I am.  When I wrote about sequencer startups back in February based on their websites, I put Stratos Genomics near the front of the pack.  Roche Molecular apparently agrees, announcing a week ago that they are acquiring Stratos.

Monday, March 30, 2020

One Gemini Celebrates Another

One of most truly useless pieces of information lodged in my brain is my zodiac sign; not once in my life have I had any interest in it.  But, given the available draws, it isn't too bad, as it's also the name of perhaps the most underappreciated engineering project of the second half of the 20th Century: Project Gemini

Saturday, March 21, 2020

1918 Flu Pandemic & Popular Culture: Take Two

My piece on the near amnesia in U.S. culture of the 1918-19 Influenza pandemic provoked a number of helpful comments, emails and conversations.  While I would stand behind the statement that it left a light footprint, there are a number of interesting cases, some of which I would never have found by conventional means.  Sometimes the collective wisdom of the internet is best for uncovering things, even when you're married to someone who catalogs books for a living.