Category Archives: Research

In the process of preparing some data for publication I needed to revisit some scripts I wrote several months ago, clean them up, and re-run them.  I was pretty amazed with how bad they were, and ended up spending a … Continue reading →

Yesterday I went to an inspiring informal seminar by Bailin Hao from Fudan University in Beijing.  Bailin presented work by his group to establish a new method for determining microbial phylogeny.  Inferring phylogeny is currently a massive headache in the … Continue reading →

**UPDATE** Got it.  You have to set the BLASTDB variable for this to work and place the taxonomy files in this same location.  I just did it in my .bash_profile: BLASTDB=”/path/to/databases” export BLASTDB **UPDATE** The original motivation for this was … Continue reading →

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 →

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 →

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 →

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 →

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 →

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 →

****************** Updated method posted here: https://www.polarmicrobes.org/?p=859 ****************** But they’re not.  Getting meaningful taxonomy from blast results is one of those things.  Here’s the situation: I ran a blastn search locally against the NCBI nt (nucleotide) database, saving the output in … Continue reading →