Author Archives: Jeff

Microbial community segmentation with R

Posted on February 2, 2017 by Jeff

In my previous post I discussed our recent paper in ISME J, in which we used community structure and flow cytometry data to predict bacterial production.  The insinuation is that if you know community structure, and have the right measure … Continue reading →

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New paper published in ISME Journal

Posted on January 20, 2017 by Jeff

I’m happy to report that a paper I wrote during my postdoc at the Lamont-Doherty Earth Observatory was published online today in the ISME Journal.  The paper, Bacterial community segmentation facilitates the prediction of ecosystem function along the coast of … Continue reading →

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paprica v0.4.0

Posted on January 8, 2017 by Jeff

I’m happy to announce the release of paprica v0.4.0.  This release adds a number of new features to our pipeline for evaluating microbial community and metabolic structure.  These include: NCBI taxonomy information for each point of placement on the reference … Continue reading →

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paprica on the cloud

Posted on November 25, 2016 by Jeff

This is a quick post to announce that paprica, our pipeline to evaluate community structure and conduct metabolic inference, is now available on the cloud as an Amazon Machine Instance (AMI).  The AMI comes with all dependencies required to execute … Continue reading →

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Antarctic Long Term Ecological Research

Posted on October 13, 2016 by Jeff

I’m very excited that our manuscript “Microbial community dynamics in two polar extremes: The lakes of the McMurdo Dry Valleys and the West Antarctic Peninsula Marine Ecosystem” has been published as an overview article in the journal BioScience.  The article … Continue reading →

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Creating a landmask for the West Antarctic Peninsula in R

Posted on September 4, 2016 by Jeff

This is going to be a pretty niche topic, but probably useful for someone out there.  Lately I’ve been working with a lot of geospatial data for the West Antarctic Peninsula.  One of the things that I needed to do … Continue reading →

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Astrobiology Primer v2

Posted on August 20, 2016 by Jeff

The long-awaited version 2 of the Astrobiology Primer was published (open access) yesterday in the journal Astrobiology.  I’m not sure who first conceived of the Astrobiology Primer, first published in 2006, but the v2 effort was headed by co-lead editors … Continue reading →

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How I learned to stop worrying and love subsampling (rarifying)

Posted on July 12, 2016 by Jeff

I have had the 2014 paper “Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissable” by McMurdie and Holmes sitting on my desk for a while now.  Yesterday I finally got around to reading it and was immediately a … Continue reading →

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Exploring genome content and genomic character with paprica and R

Posted on July 7, 2016 by Jeff

The paprica pipeline was designed to infer the genomic content and genomic characteristics of a set of 16S rRNA gene reads.  To enable this the paprica database organizes this information by phylogeny for many of the completed genomes in Genbank.  … Continue reading →

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The 6 cent speeding ticket

Posted on June 17, 2016 by Jeff

I’m going to go way off the normal track here and do a bit of social commentary.  I heard a radio piece on my drive home yesterday about the challenge of paying court and legal fees for low income wage … Continue reading →

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