Author Archives: Jeff
Budget Woes
Everyone’s impacted by the shutdown in the federal government in some way. First and foremost are federal employees, including research scientists at NOAA, NASA, and the other research-minded federal agencies. Not only are these individuals locked out of their workplaces, … Continue reading
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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
