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Recent Posts
- Local installation of DeepTMHMM December 3, 2025
- A simple solution for continuous, real-time monitoring with the Seabird SUNAV2 over RS232 March 22, 2025
- New postdoctoral position in pathogen ecology September 25, 2024
- Seeking postdoc in phytoplankton ecology August 27, 2024
- Recent blog post by PhD student Beth Connors February 13, 2024
- New paper: Antarctic metagenomes reveal novel microbial diversity May 19, 2023
- New postdoctoral research opportunity! April 7, 2023
- Alignment and phylogenetic inference with hmmalign and RAxML-ng May 31, 2022
- New paper on using machine learning to predict biogeochemistry from microbial community structure February 12, 2022
- Lab manager position open! January 15, 2022
Author Archives: Jeff
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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AAAS-CASE
I’m currently in Washington, DC for the pilot AAAS-CASE (Catalyzing Advocacy and Science in Engineering) workshop. I wanted to share a great short video that was sent to the attendees before the workshop. http://www.innovationdeficit.org/ The video describes the “innovation deficit”, … Continue reading
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Converting pfams to cogs
Anyone with a sequence to classify faces a bewildering array of database choice. You’ve got your classic NCBI quiver; nt, nr, refseq, cdd, etc. Then you’ve got uniprot, seed, pfam, and numerous others. Some of these have obvious advantages or … Continue reading
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Where goes the carbon in the Palmer LTER?
In the last post I broadly described some of the ecological changes underway in the Palmer LTER. If we consider only the biological components of any ecosystem (excluding the chemical and physical components) we can diagram their interactions as a … Continue reading
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A cruise in the Palmer LTER
For the last five weeks I’ve been on a research cruise aboard the ARSV Laurence M. Gould off the west Antarctic Peninsula (WAP). This region has received a lot of attention in recent years as one of the fastest warming … Continue reading
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Android, Mendeley, Referey, and taming the reference beast
Like everyone else in Academia I’m in a constant struggle against information overload. This comes not only from the overwhelming amount of data from analyses I’m working on, but from an ever-growing stream of scientific literature. I gave up trying … Continue reading
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Frost flower metagenome paper submitted
I just hit the “submit” button for our latest frost flower paper, which reviewer-be-willing will appear in an upcoming polar and alpine special issue of FEMS Microbial Ecology. Several scattered bits of analysis from the paper have appeared in this … Continue reading
Maintaining an updated record of Genbank genomes
For an ongoing project I need a local copy of all the prokaryotic genomes in Genbank. New genomes are being added an an ever-increasing rate, making it difficult to keep up by manually downloading them from the ftp site. I … Continue reading
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Online bioinformatics courses
Speaking of the UW Oceanography Bioinformatics Seminar… one of the seminar participants just sent around a Plos Computational Biology that lists a complete curriculum’s worth of free online bioinformatics courses. Some of the courses are more suitable for computer scientists … Continue reading
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