Author Archives: Jeff

Entry-level computers for bioinformatics

Posted on June 9, 2013 by Jeff

When I started graduate school I new absolutely nothing about computing on anything more high performance than a laptop.  I assumed that clusters and servers were exclusive to large, well-funded labs.  Access to these items is a huge limiting factor … Continue reading →

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Video output from R script

Posted on June 1, 2013 by Jeff

As an offshoot from one of my dissertation projects I’m developing a simple model to explore protein evolution.  The model takes an amino acid sequence and mutates it, selecting for mutations that result in improvement for one of several measurable … Continue reading →

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Nathaniel B. Palmer time lapse

Posted on May 14, 2013 by Jeff

This time lapse video was recently forwarded to me, taken from the deck of the NSF research vessel Nathaniel B. Palmer during a cruise through the Ross Sea.  It’s entertaining, and illustrates the wide diversity of sea ice that can … Continue reading →

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Land of Lakes

Posted on May 10, 2013 by Jeff

We just finished a crazy few days of sampling and I’m only now, back in Seattle, getting a moment to assimilate all of it.  The Icy World team from JPL arrived late in the day on May 1, and we … Continue reading →

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Cracks in the ice

Posted on May 3, 2013 by Jeff

We made another effort at reaching the ice edge last night, but things have gotten a little odd out there.  About 500 meters short of the ice edge we encountered some of the whaling crew hanging out around a 2 … Continue reading →

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Breaking ice in the hot sun…

Posted on May 1, 2013 by Jeff

I fought the ice and the ice won?  Had a long, good day on the ice yesterday (and yes, it was quite hot).  There was a little chaos at the start, as there always is.  Barrow depends in no small … Continue reading →

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Barrow or Bust!

Posted on April 29, 2013 by Jeff

I’ll be taking off for Barrow in just a few hours, the last field effort of my dissertation – and my last chance at collecting frost flowers!  This will be my 6th trip up in the last four years, although … Continue reading →

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Greenland might not be green…

Posted on April 17, 2013 by Jeff

But you can grow flowers there. As readers of this blog know, one of the Deming Lab’s major research directions is the microbiology of the sea ice surface – frost flowers, saline snow, and related features.  Since the sea ice … Continue reading →

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Comments now open

Posted on April 13, 2013 by Jeff

A while back I deactivated comments and registration due to excessive spam.  After getting a great comment via email from a researcher at UCSF regarding the NCBI taxonomy parsing article (suggesting the use of Python primary keys to speed up … Continue reading →

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A little Europa here in Washington

Posted on April 12, 2013 by Jeff

I got an email the other day from a colleague who teaches science at Soap Lake High School, a rural high school in eastern Washington that, in my opinion, punches above its weight in the sciences.  One of his students … Continue reading →

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