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 …
We’d like to first thank Jon for the opportunity to discuss our work in this forum. We recently published a study investigating direct functional annotation of short metagenomic reads that stemmed from protocol development for our lab. Jon invited us to write a blog post on the subject, and we thought it would be a …
Got this in an email from the Bioinformatics Core at the Genome Center. I saw a lot of these mistakes in an NSF Biodiversity panel that I served on earlier this year. One thing I disagree with is the notion that you cannot do bioinformatics on a personal computer. I do this all the time. …
If you’ve been reading our posts, you are quite familiar with our efforts at characterizing the bacterial and fungal communities of the built environment. We’ve described our study design, experimental protocols, and results. One thing we may have left you wondering about, however, is the nuts and bolts behind the analyses we and other MoBe …
Posted a request for help on Twitter but I thought it might be of interest to some other people so am also posting about it here. Basically what we (me and Lizzy Wilbanks in my lab) is to take some microbial genomes and to fully annotate all of the repeat elements and all of the …
You can download the database of over 360 publications that report characteristics of the indoor environment along with the microbes found in the studies. Each publication is entered as a record and includes citation, abstract, keywords, organisms, substrates, and environmental conditions as reported by the authors. The database in MS Access format is searchable for …