Category Archives: Research

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 →

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 →

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 →

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 →

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 →

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 →

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 →

UW Oceanography has a student-lead bioinformatics seminar that meets every spring and fall (or at least has since the fall of 2012 – we hope to continue it).  Each quarter is a little different, this time around each seminar attendee … Continue reading →

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 →

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 →