Author Archives: Jeff
paprica v0.4.0
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
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
Antarctic Long Term Ecological Research
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
Creating a landmask for the West Antarctic Peninsula in R
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
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)
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
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
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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The Database Dilemma
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
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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