IRIS AI and a wondrous rabbit hole of a labelled network of scientific papers

Got an email from the developers of IRIS AI the other day: And decided to play around with it. So I went to our Zotero collection on microbiology of the built environment: From there I got a paper and found it’s URL: Meadow, J. F., Altrichter, A. E., Kembel, S. W., Kline, J., Mhuireach, G., Moriyama, M., Northcutt, …

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 …

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 …

Announcing the scikit-bio cookbook “recipe-of-the-week” series

scikit-bio is a library for building bioinformatics tools and workflows in Python. It’s already a core dependency of QIIME, is extensively used in An Introduction to Applied Bioinformatics, and was the subject of my talk at SciPy 2014 (video) this past July. One of our focuses with scikit-bio is to make its functionality very accessible …

Lessons Learned from Building an Interdisciplinary Scientific Community in the Online Sphere

The Microbiology of the Built Environment Network (http://microBE.net – this website) has made it into the community page at PLoS Biology! Our article has been in the works for some time, and we’re now pleased to announce its official publication: Bik HM, Coil DA, Eisen JA (2014) microBEnet: Lessons Learned from Building an Interdisciplinary Scientific Community …

Follow new pubs/citations on Google Scholar Citations pages to stay up to date on a field

At a recent meeting of the Sloan Foundation program on Microbiomes of the Built Environment I gave a talk about microBEnet and kind of begged people in the program to send me emails when they had new papers out so we could include them in our reference collection and could blog about them.  And one …

Wanted – suggestions for alternatives to Mendeley (socially aware reference collections)

So – my microBEnet project has spent a lot of time working on this reference collection that we have currently in Mendeley. Microbiology of the Built Environment | Mendeley Group. In addition to just collecting these 700+ papers we have also added our own tags to the references in regard to the types of environments …