Gearing up the UNITE database for the built mycobiome

Gearing up the UNITE database for the built mycobiome The team behind the UNITE database for molecular identification of fungi has been granted support from the Sloan Foundation to strengthen the support for fungi from the built environment. Launched in 2001 as an ITS database for identification of ectomycorrhizal fungi in the Nordic countries, UNITE …

CAMI Challenge is Now Open for Participation

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 …

MicrobiomeDigest – your daily fix of microbiome literature

Microbiomes are everywhere. Not only inside and around us, but also in the scientific literature. Not too many years ago, only a handful of microbiology laboratories were analyzing the composition of the invisible communities that surround us. Today, it feels as if every other scientist is doing something microbiome-related. New techniques such as high-throughput sequencing and …

The Initiative for the Critical Assessment of Metagenome Interpretation (CAMI)

In just over a decade, metagenomics has developed into a powerful and productive method in microbiology and microbial ecology. The ability to retrieve and organize bits and pieces of genomic DNA from any natural context has opened a window into the vast universe of uncultivated microbes. Tremendous progress has been made in computational approaches to …

Genomic data sharing via BitTorrent, part 2 – BioTorrents to BitTorious

As someone who uses sequence data for most of my research,  I am continually happy with the fact that sequencing continues to get cheaper and easier and faster and bigger and better and more and more and more.  Along with such continued advances, sharing the data produced by such sequencing has become somewhat challenging at …

Nice resource: BRIK – Building Research Information Knowledgebase

Recently I participated in the Society for Building Science Educators (SBSE) annual retreat (more about this soon).  And at the retreat I saw a fascinating presentation rom Richard L. Hayes who runs helps facilitate something called the Building Research Information Knowledgebase (aka BRIK). BRIK is a “collaborative effort of the American Institute of Architects and the National Institute …

Thank you ISIAQ for the “Vocabulary of the Indoor Air Sciences” #microBEnet

One reason that it can be difficult to bridge across different fields is just learning the vocabulary and jargon of the field.  So happy to have found this: Vocabulary of the Indoor Air Sciences while browsing the web site for ISIAQ – the International Society of Indoor Air Quality and Climate. It even has 43 …

“Crowd-sourced” microbial community info transfer plus link to SIB Bioinformatics Resource portal

One of the unmet challenges to the Sloan Foundation’s Microbiology of the Built Environment (MoBE) program is the sharing of the results of the Foundation-funded studies as well as other studies of the indoor and built environment microbiome. At the American Society for Microbiology’s annual conference in Boston last week, I was impressed by Pieter …

Microbes and the design of animal shelters

Animal shelters provide an essential and beneficial social service, caring for an estimated 9 million pets each year in the United States. Many animals entering a shelter are highly stressed and lack the benefits of standard veterinary care, including vaccinations. Moreover animal shelters are an intensive housing situation that amplifies the transmission of infectious diseases …