Workshops

Throughout 2020, Pat will offer workshops on mothur and programming in R for microbial ecologists. These will all be offered online via zoom. If you are interested in attending and would like to register or get more information about fees and specifics, please email him his gmail account (userid: pdschloss). Other workshops will be announced throughout the year.

  • June 21-24: mothur workshop (10 PM-3 AM EDT (GMT-400) - designed for people in Eastern Hemisphere)
  • July 15-17: Microbial Ecology R workshop (9 AM-4 PM EDT (GMT-400))
  • August 12-14: mothur workshop (9 AM-4 PM EDT (GMT-400))

General R Workshop

This workshop is being filled on a first come, first served basis. The workshop is geared towards people who would like to learn R or to learn it better using a diverse collection of datasets. This workshop is intended for beginners and more advanced R programmers who would like to fill their gaps in knowledge. I assume no previous computer programming experience. The workshop is an even blend of lecture/discussion and hands on use of R with real data. The material is centered on learning how to solve problems using functions from the “tidyverse”. The workshop will give you a pretty thorough set of working examples for how to use packages like ggplot2, readr, dplyr, stringr, and lubridate. More importantly, the workshop will emphasize developing problem solving skills for solving data and programming problems. The materials can be found on the Riffomonas website

mothur workshop

This 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
  • Amplicon sequence variants
  • OTU identification
  • Sequence/OTU classification

Day 3:

  • Intro to microbial ecology
  • Methods of measuring alpha and beta diversity
  • Population level analyses

The workshop is an expanded discussion on the MiSeq SOP.

Microbial Ecology R Workshop

This workshop is being filled on a first come, first served basis. The workshop is geared towards people with interests in microbial ecology that would like to learn R or to learn it better 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 R with real data and typically uses mothur output files as a starting point. It is taught around the generation of data visualization methods commonly used by microbial ecologists. Along the way we’ll learn a number of ways to work with data from within R. Here is a rough outline of what the workshop schedule will look like (it is subject to some minor changes)...

  • Ordination
  • Stripcharts and box and whisker plots
  • Line plots
  • Barcharts
  • Subsetting data
  • Reading and writing data
  • Basic parametric and non-parametric analyses

The workshop will give you a pretty thorough set of working examples for how to use packages like readr, dplyr, and ggplot2 with data from mothur; however, prior knowledge of mothur is not a prerequisite. The materials we will follow are available on the Riffomonas website