Author Archives: Jeff
Basic computers for bioinformatics, revisited
I recently started a postdoc in a lab without any real computer infrastructure so I was in need of a system with a little more juice than my laptop. While a graduate student at the UW I did everything except … Continue reading
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Future of ice jobs at the UW
There are two great polar ecology jobs posted at the University of Washington right now. It’s rare to find academic jobs specific to the polar regions so this will be a great opportunity for someone out there! The new positions … Continue reading
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In defense of observations
This week I’m at the biennial meeting of the International Society of Microbial Ecologists (ISME) in Seoul. During lunch yesterday there was a special “bird’s eye view” talk given by Dr. James Prosser, a preeminent microbiologist from the University of … Continue reading
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The history of sea ice microbial ecology
Doctoral dissertations typically include an introduction, a Chapter 1 that summarizes the work and the motivation for undertaking it. Last week I submitted my dissertation to the UW and the introduction, which includes citations from some long-ago work on psychrophiles … Continue reading
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Clustering metagenomic sequence reads
Another interesting paper caught my eye last week, Nielsen et al. in Nature Biotechnology; Identification and assembly of genomes and genetic elements in complex metagenomic samples without using a reference genome. First, a complaint: 53 authors, really? There are more … Continue reading
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Great modeling paper published
A very nice paper in the ISME Journal came across my Google Scholar alerts this week – Satellite remote sensing data can be used to model marine microbial metabolite turnover, by Larsen et al. The author list includes some heavy … Continue reading
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New website address!
Pending the (hopeful) defense of my dissertation on August 8th I’ll be starting a postdoc at the Lamont-Doherty Earth Observatory at Columbia University. Since there’s generally a little downtime between turning in a thesis and defending it I’ve migrated this … Continue reading
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Some thoughts on modeling
I’m not a modeler, but I played one once in grad school. Or at least that’s how I’m feeling at the moment. I’m currently working on the last chapter of my dissertation and it became necessary to explore the mechanisms … Continue reading
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Making maps in R
I don’t have a lot of experience with geospatial data analysis but following a recent cruise I had the need to plot some geospatial data. The go-to program for this seems to be Matlab (or even ArcGIS, for those who … Continue reading
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Dispatch from AAAS-CASE
As mentioned in my previous post I spent the last three days at the AAAS-CASE workshop in Washington, DC. The purpose of the workshop was to introduce junior scientists to the legislative process and the ins and outs of science … Continue reading
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