Author Archives: Jeff

The Database Dilemma

Posted on May 25, 2016 by Jeff

Microbial ecologists know they have a problem with data archiving, particularly when it comes to sequence data.  I’m not entirely sure why this is the case; in theory it would be pretty straightforward to build a database searchable by the … Continue reading →

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Roadmap to Ocean Worlds: Polar microbial ecology and the search for totally normal life

Posted on May 16, 2016 by Jeff

Recently congress recommended that NASA create an Ocean Worlds Exploration Program whose primary goal is “to discover extant life on another world using a mix of Discovery, New Frontiers, and flagship class missions”.  Pretty awesome.  In February I was invited … Continue reading →

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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 →

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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 →

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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 →

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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 →

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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 →

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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 →

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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 →

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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 →

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