Author Archives: Jeff

Phylogenetic placement re-re-visited

Posted on May 13, 2016 by Jeff

I use phylogenetic placement, namely the program pplacer, in a lot of my publications.  It is also a core part of of the paprica metabolic inference pipeline.  As a result I field a lot questions from people trying to integrate … Continue reading →

Posted in Research | 20 Comments

Another victim of science funding

Posted on April 12, 2016 by Jeff

Or rather the lack thereof.  I was very disappointed to receive an email yesterday that BioCyc, a popular database of enzymes and metabolic pathways in model organisms, is moving to a subscription model.  The email is posted below in its … Continue reading →

Posted in Uncategorized | Leave a comment

Tutorial: Annotating metagenomes with paprica-mg

Posted on March 26, 2016 by Jeff

This tutorial is both a work in progress and a living document.  If you see an error, or want something added, please let me know by leaving a comment. Starting with version 3.0.0 paprica contains a metagenomic annotation module.  This … Continue reading →

Posted in paprica | Leave a comment

Antarctic wind-driven bacterial dispersal paper published

Posted on March 24, 2016 by Jeff

I’m happy to report that one of the appendices in my dissertation was just published in the journal Polar Biology.  The paper, titled Wind-driven distribution of bacteria in coastal Antarctica: evidence from the Ross Sea region, was a long time … Continue reading →

Posted in Research | Leave a comment

Tutorial: Building the paprica database

Posted on March 11, 2016 by Jeff

This tutorial is both a work in progress and a living document.  If you see an error, or want something added, please let me know by leaving a comment. Building the paprica database provides maximum flexibility but involves more moving … Continue reading →

Posted in paprica | Leave a comment

Correctly evaluating metabolic inference methods

Posted on March 4, 2016 by Jeff

Last week I gave a talk at the biennial Ocean Sciences Meeting that included some results from analysis with paprica.  Since paprica is a relatively new method I showed the below figure to demonstrate that paprica works.  The figure shows … Continue reading →

Posted in paprica | Leave a comment

Tutorial: Analysis with paprica

Posted on January 25, 2016 by Jeff

This tutorial is both a work in progress and a living document.  If you see an error, or want something added, please let me know by leaving a comment. Getting Started I’ve been making a lot of improvements to paprica, … Continue reading →

Posted in paprica | 11 Comments

Tutorial: Installing paprica on Mac OSX

Posted on January 20, 2016 by Jeff

The following is a paprica installation tutorial for novice users on Mac OSX (installation on Linux is quite a bit simpler). If you’re comfortable editing your PATH and installing things using bash you probably don’t need to follow this tutorial, … Continue reading →

Posted in paprica | 1 Comment

Wrapping up the season

Posted on December 23, 2015 by Jeff

Yesterday morning the Gould returned to Palmer Station, which means that it’s time for Jamie and I to take off. I’m looking forward to getting home and working through all the data we’ve collected (and who wouldn’t want to spend … Continue reading →

Posted in Palmer 2015 field season | Leave a comment

Making sense of megafauna: The canyon hypothesis

Posted on December 13, 2015 by Jeff

Earlier in the week we had our orca show, yesterday this was the view of the top of our boat ramp: In fact that view hasn’t changed.  From the science office I can just make out the penguin colony on … Continue reading →

Posted in Palmer 2015 field season | 2 Comments