Rebranding of MICRBIOL 612

Dec 16, 2015

During the winter semester, Pat and Evan Snitkin will be teaming up to teach a new version of MICRBIOL 612: Microbial Informatics. Instead of being a single semester-long course, the content will be divided into three 3-day long workshops. The duo plans on offering the course each semester with a different combination of courses each semester. They hope that this new format will be more attractive to senior graduate students, postdocs, and other researchers who don’t have the ability to take a traditional course.

In the fall semesters of 2012 and 2014 Pat offered a semester-long course - Microbial Informatics (MICRBIOL 612). This course was primarily an R programming course with a heavy dose of statistics and microbiology and immunology data analysis. There was a lot of interest in the material, but the semester-long format made difficult for people to make the extended time commitment. Starting the winter semester of 2016 they are going to change the format of the course to better serve students and other researchers on campus. Pat and Evan will be offering the course for variable credit each semester as a series of 2 or 3 full day workshops. Those interested in taking the course for credit will complete a capstone project for each workshop.

In the winter semester they will be offering the following…

612.1 Introduction to data analysis (Schloss & Snitkin) - February 29-March 2 - 1 credit - Furstenberg 2710 This module will introduce participants to the best practices in setting up and running projects that involve data analysis with an eye towards automation and reproducibility. Tools covered will be bash, git and introductory SQL and R. The content largely overlaps with that of Software Carpentry workshops. Prerequisites: None

612.2 Microbial community analysis with mothur (Schloss) - April 13-15 - 1 credit - Furstenberg 2710 In this module participants will use the popular mothur software package to analyze microbial community data. Participants will also learn how to use the flux high performance computing cluster to facilitate their analysis. Prerequisites: 612.1 or recent participation in a Software Carpentry workshop

612.3 Microbial genomics analysis (Snitkin) - Dates - March 28-30 - 1 credit - Furstenberg 2710 This module covers the basics of microbial genomic analysis using publicly available tools that are commonly referenced in genomics literature. Students will learn the steps and associated tools that are required to process, annotate and compare microbial genomes. Prerequisites: 612.1 or recent participation in a Software Carpentry workshop

Their current plan is to offer 612.1 every semester plus one or two additional modules along similar themes as 612.2 and 612.3. The modules will be capped at 25 participants with those taking the modules for credit given priority.