Author Archives: Jeff
A new model for scientific careers
Traditionally there were three ways that, having acquired a PhD, a researcher could continue with their scientific career: 1) Seek a faculty job at an academic institution (typically a university). University jobs are wonderful in that they allow for complete … Continue reading
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Risk in Research
The polar research community was reminded of the risks in polar research yesterday with the news that a helicopter crash had killed two Canadian Coast Guard officers, including the commander of the venerated research icebreaker CCGS Amundsen, and scientist Klaus … Continue reading
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Halocarbons from young sea ice and frost flowers
An interesting paper come out recently by a group at the University of Gothenburg in Sweden. Working at Svalbard, a common Arctic study site for European researchers, they measured the flux of organic compounds called halocarbons (or organohalides) from young … Continue reading
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Compositional vectors revisited
A couple of articles back I posted a down-and-dirty method for calculating compositional vectors in a whole genome. I’m using compositional vectors in one of my projects so I reworked the code to make the analysis more rigorous, implementing the … Continue reading
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Top 10 scripting tricks for basic bioinformatics
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
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The future of phylogeny
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
Somethings should be easy, and they are…
**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
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A particularly bad idea
I haven’t written many posts on this blog that are political in nature, in fact I think the only political topic that’s come across is the need for new investment in the US ice breaker fleet. A particularly troubling bill … Continue reading
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Entry-level computers for bioinformatics
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
Video output from R script
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
