Microbiome Bioinformatics with QIIME 2 workshop, June 21-23 2017 in Las Vegas, NV

Members of the QIIME development group, led by Greg Caporaso, will teach a three-day workshop on bioinformatics tools for microbial ecology. The workshop will include lectures covering basic QIIME 2 usage and theory, and hands-on work with QIIME 2 to perform microbiome analysis from raw sequence data through publication-quality statistics and visualizations. This workshop will …

QIIME 2 workshop Nov 4-5 (just prior to SSSA meeting) in Phoenix, AZ

Members of the QIIME development group, led by Greg Caporaso and Antonio Gonzalez, will teach a two-day workshop on bioinformatics tools for microbial ecology. The workshop will include lectures covering basic QIIME usage and theory, and hands-on work with QIIME to perform microbiome analysis from raw sequence data through publication-quality statistics and visualizations. The workshop …

Caporaso Lab is hiring a software engineer to work on QIIME and scikit-bio

Now that QIIME 2 is officially funded (see my recent announcement here on the American Gut Blog), the Caporaso Lab at Northern Arizona University is hiring a new full-time developer to work on QIIME, scikit-bio, An Introduction to Applied Bioinformatics, and our many on-going microbiome analysis projects. The official job posting is available here, and you can …

Request for comments on scikit-bio: should we drop support for Python 2 in favor of Python 3 only?

scikit-bio is a library implementing core bioinformatics algorithms and data structures, and providing support for bioinformatics data munging. You can learn more about the project by watching Jai Rideout and Evan Bolyen’s 20 minute SciPy 2015 talk. scikit-bio currently supports Python 2 (i.e., Legacy Python) and Python 3. We’re considering dropping support for Python 2, …

Update on An Introduction to Applied Bioinformatics

About a year ago, I posted here about my free, interactive text: An Introduction to Applied Bioinformatics. The project is now Sloan-funded (as of April 2015), so there will be a lot of changes and expanded content coming down the pipe over the next few months. One major change that went in recently, and which …

SciPy 2015 Computational Life and Medical Sciences Mini-Symposium: Call for Abstracts

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 …

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 …