As the snow piles up and the temperature falls, there are days when this sabbatical feels more like a monastic retreat. I am even more grateful for my electronic network of colleagues on those days. Reading Pauline's post on her first month of sabbatical made me realize a few things.

  1. Posting every week on my progress is probably going to discourage more than encourage me due to the ebb and flow of research.
  2. I really wish I had a "sabbatical office" out of the path of students but still in the path of other faculty.
  3. I need to decide not to do things.

On that note, here's what I've been doing since my last update.

  • Got my workstation set up with the software I need and started analyzing the first data set with an eye toward automation. Unsurprisingly, the steps I have scripts for feel solid, the rest is a bit of a mess. At first glance it looks like read trimming is mostly CPU bound, while kmer counting is i/o bound. I can't do much about CPU right now, so I ordered a 500GB SSD scratch disk. The hope is to fetch, trim and count on the scratch disk and sync the results back to the RAID disks.
  • Assembled the PC for the MinION and installed the necessary software. Debating whether I should set it up in the home office or not. If I ever get access to the user support forum I'll see how much equipment I need to run it. If I can work up the sample in the lab & then take it home with a P-200, sold.
  • Taught a Software Carpentry workshop at the University at Albany. I always have a good time teaching these workshops, but this one was particularly fun. Our hosts were extremely well prepared, our helpers were top notch, and there were none of the usual hiccups with WiFi or software installation. My co-teacher, Thomas Guignard, took some photos of the interesting campus architecture, which you can view on his site. I really enjoyed teaching with him and he confirmed that in my next life, I want to be a librarian.
  • Swore repeatedly at the Allentown Public School Board for canceling and/or delaying classes at the threat of snow. That I was single parenting due to my spouse being out of town made it especially relaxing.

Then again, there were snow people to be had.


Sabbatical report: January

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