February mothur workshop #microbes #diversity

Posting this which I got from the Mothur mailing list

Thanks for your continued support of mothur. From first hand experience, I know that PIs tend to be very generous around the holidays. With that in mind, I’m happy to announce that the next mothur workshop will run from February 8 to 10, 2016 near the Detroit airport. How about asking your PI if they’ll send you to the workshop? Of course, generous PIs are also most welcome to come as well! The workshop is being filled on a first come, first served basis. The workshop is geared towards people with diverse backgrounds so you shouldn’t feel like this isn’t for you if you are a beginner. I assume no previous computer programming experience. The workshop is an even blend of lecture/discussion and hands on use of mothur with real sequence data. Here is a rough outline of what the workshop schedule will look like (although it is subject to some minor changes)…

Day 1:
– Overview of methods used in microbial ecology
– DNA sequencing technologies (Sanger, 454, Illumina, IonTorrent, PacBio)
– Introduction to mothur, command line interface, and GUI
– Improving sequence quality
– Alignment

Day 2:
– Chimera detection
– Distance calaculations
– OTU identification
– Sequence/OTU classification

Day 3:
– Intro to quantitative ecology for microbial ecologists
– Methods of measuring alpha and beta diversity
– Population level analyses

Basics: As indicated above, each day there will be a lecture and discussion interspersed with hands-on activities and it will run from 9 to 5. If you would like to meet with me one-on-one to discuss your project, I can do that in the evening and during breaks.

To bring: It is important that you bring a laptop to the workshop. While it would be helpful if you came with mothur pre-installed, it is not that important since we can do this at the workshop. People often find it helpful to bring along their own data to play with after they have mastered the examples I provide. People also find it helpful to bring a notebook for taking notes during the lecture components. Of course, a willingness to learn, questions, and a good sense of humor are essential!

For further details on costs and logistics, feel free to send me an email.

Happy Holidays,
Pat Schloss

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.