This is a story of my first involvement pushing a publication that wanted to be University owned “all rights reserved” to becoming one released under a Creative Commons license. I’m not sure that the arcane details will be of interest to many people, but I think there’s an important lesson here about sticking to your …
A few weeks ago we wrapped up Spring Quarter here at UC Davis and the end of our experimental “Swabs to Genomes” class, taught as a freshman seminar. As we introduced here, the idea was to take a set of students from colonies on a plate (from a swab) through a collection of ready to …
Back in September 2014 I was invited to write a book chapter on citizen science in microbiology. After several iterations of the book, the chapter, and the licensing agreement here is the final version. The book came out yesterday, here’s a link to the entire book on Amazon (“The Rightful Place of Science: Citizen Science“) …
Week 10 was the last week of class (that’s a quarter system for all semester-types out there). In the previous class the students got together in groups and produced “consensus” genome announcements for their groups. In the intervening week, Ashley and I produced a “consensus consensus” Genome Announcement, taking pieces from the various groups. Then …
Here’s my report from Day 2 of the Microbiology of the Built Environment Conference in Boulder… the 5th annual and last of its kind! Storify of the tweets from the day below. The opening talk on Day 2 was by Martin Taubel from the National Institute for Health and Welfare, Finland, “Of house dust and …
The blog posts for the previous 8 weeks were written as group assignments by the students taking this “Swabs to Genomes” class. For the final two weeks of the quarter, I will just briefly describe what we did on those days. Based on the results from Phylosift, A5-miseq, and RAST we made a call at …
(this blog post was written by group #4 as a writing assignment) Our goal for this week’s lesson was to double check that the genome we sequenced is, in fact, the organism we are interested in. After uploading our sequences up to RAST last week, we found out the results and were able to look …
Here’s the report from Day 1 of the 5th annual Microbiology of the Built Environment meeting in Boulder, CO. Following my summary of the talks is a Storify of all the tweets from the day. The first talk of the day was by Ulla Haverinen-Shaughnessy from the University of Eastern Finland whose talk was entitled …
(this blog post was written by group #3 as a writing assignment) Last week in class we were introduced to genome assembly and validation by using an open-source bacterial genome assembly program A5-miseq. This program produces high quality genome assemblies by automating processes such data processing, error correction, contig and scaffold assembly, and final verification. …
(This post was written by group #2 as a writing assignment) Since we were about half way through this quarter, the activity we did this past week was to summarize all the experiments we have performed so far, list the consumable materials that were used, and any questions or concerns that may have arisen during …