Author Archives: Jeff

AAAS-CASE

Posted on March 30, 2014 by Jeff

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

Posted on March 9, 2014 by Jeff

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?

Posted on February 19, 2014 by Jeff

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

Posted on February 11, 2014 by Jeff

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

Posted on December 19, 2013 by Jeff

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

Posted on November 19, 2013 by Jeff

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 →

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Maintaining an updated record of Genbank genomes

Posted on November 7, 2013 by Jeff

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

Posted on October 16, 2013 by Jeff

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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Phylogenetic Placement Revisited

Posted on October 14, 2013 by Jeff

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 →

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Budget Woes

Posted on October 8, 2013 by Jeff

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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