Author Archives: jennomics

About jennomics

I am a Postdoc in Jonathan Eisen's Lab at UC Davis. jennomics@gmail.com

installing STAMP on a Mac

Since this was such a huge pain in the ass for so many of us, I figured I’d share what finally worked for me. First this: pip install STAMP then I got an error about matplotlib, so then this: pip … Continue reading

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What the fungi do I do with my ITS library? (Part 2)

What the fungi do I do with my ITS library (Part 2) Originally posted on jennomics.com on May 22, 2014 Previously, I expressed some concern about size variation in my environmental fungal ITS PCR libraries. I’m still concerned about that, … Continue reading

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What the fungi do I do with my ITS library?

Originally posted on jennomics.com May 21, 2014 It’s been about 8 years since I started working on my first 16S rRNA PCR survey (of Drosophila gut microbes). At that time, I was occasionally asked, “what about Archaea or what about … Continue reading

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Valentine’s Day Seminar at #UCDavis: Herbert M Sauro: Reproducibility in Systems and Synthetic Biology: Issues at the bench and the computer.

The Genome Center Biological Networks Seminars Series present: Reproducibility in Systems and Synthetic Biology: Issues at the bench and the computer. Speaker: Herbert M Sauro Associate Professor Department of Bioengineering University of Washington Date: Friday, February 14th, 2014, 10am – … Continue reading

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NASA Data Bridge Workshop

I’m at Caltech right now, at a workshop designed to figure out how to use citizen scientists to bridge the gap between NASA Earth Science data and societal needs (policy, management, forecasting, etc.) I’ll write up a more detailed summary … Continue reading

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Citizen (Funded) Science

As evidenced by the buzz around the Citizen Science session at ASM yesterday, microbial ecologists are increasingly looking for ways to engage “Citizen Scientists” to participate in large-scale projects, often by crowd-sourcing sample collection. This concept is not new; in … Continue reading

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UC Davis’ 2nd Annual BioBlitz will be sampling MICROBES!

The first-ever MicroBioBlitz will be held tomorrow, April 27th, from 9am-2pm! Join the Eisen Lab and the UC Davis chapter of SEEDS (the Ecological Society of America’s Undergraduate Ecology Club) at the Putah Creek Riparian Reserve for their second annual … Continue reading

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Fryxell subsampled data and PhyloSift results

Jonathan has made available 50,000 reads from each of the Fryxell libraries here. Just in case you find this useful for testing. Also in this folder, there are PhyloSift results for each library (SampleAnt1-5).

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Annotation Databases

MG-RAST allows you to view the annotation of your data using several different annotation pipelines/databases. So, we had a discussion about them. Each database/tool was tackled by a different person: 1. GenBank/RefSeq – Joe 2. SEED/Subsystems – Jenna 3. COG/NOG/eggNOG … Continue reading

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Metagenomics Working Group – notes from 4/12/13

Guillaume ran us through the MG-RAST interface Question that came up again (to be asked at the QIIME workshop) – what is the difference between PCA and PCoA Canonical Correlation Analysis – a way to put vectors on your PCA … Continue reading

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