Suppose you owned a warehouse that serves as a distribution hub for grocery stores, and you find that every so often, someone is pooping in your warehouse. Not only is that insulting and obnoxious, but it also has the potential to make a lot of people very sick. You take the shift schedule, and you correlate …
So … what goes around comes around. In 2003 and 2004, I spent a lot of time discussing and arguing with people about what would be the best strategy for making and sequencing Sanger libraries for metagenomic sequencing for the Sargasso Sea metagenome study coordinated by the Venter Institute (I worked at TIGR at the time and …
There is a new #openaccess paper out that may be of interest to many working on microbes in the built envronment or microbes in air (indoors or outdoors): Challenges and Opportunities of Airborne Metagenomics by Behzad et al. in Gebome Biology and Evolution. There are some useful things in this paper and some strange things but …
There are few constants in this world. One exception, however, is the passing of day to night, which has gone on without fail since life first emerged on Earth. Early life quickly learned to anticipate changes associated with light and dark. This ability to tell time – to peer into the immediate future – was …
Just got this announcement by email and I thought it might be of interest: Join the curation effort & enroll in our first workshop! What: Workshop to produce curated 18S rDNA reference database. When: July 19th — 25th, 2015. Where: Vancouver, Canada on the University of British Columbia campus. How much: We will cover the cost of housing, breakfast and …
Well, I have been digging around a lot into Nanopore sequencing recently. This started as preparation for a lecture I gave at the Bodega Applied Phylogenetics course a few weeks ago on “The Evolution of DNA sequencing.” In preparation for my talk I posted my slides from last years talk and asked people on Twitter …
Dear metagenome method developers, The first challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI) begins right now! Over the last three months, we received valuable feedback from the community playing with our toy data sets. We incorporated many of your suggestions, thanks again! Today, we proudly release the official data sets …
SciPy 2015 (Scientific Computing with Python) is coming up in Austin, TX this July 6-12. I attended SciPy last year for the first time to present on scikit-bio (see my talk here), and thought it was an excellent meeting. It was great to spend a week talking about software and software development, which isn’t the …
Have you ever wondered what’s in the air of a daycare center, where kids swap microbes every day? A team from Virginia Tech and the University of Pittsburgh is investigating the viral ecology in air of a daycare center using metagenomics. We have collected samples on HVAC filters and are looking for a sequencing core …
A recent post highlighted issues with analyzing fungal ITS data, and that inspired my labmate Sydney Glassman and me to want to share our experiences with using amplicons to characterize fungal communities. We are very excited that people are interested in delving into the wonderful world of fungi, and we wish to share our love …