We will be offering mothur and R workshops throughout 2019. Learn more.

Workshops

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Throughout 2017, Pat will offer 5 workshops on mothur, programming in R, and reproducible research for microbial ecologists. 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)

  • January 23-25: R
  • April 3-5: mothur
  • May 8-10: Reproducible research
  • August 28-30: R
  • November 27-29: mothur


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
  • OTU identification
  • Sequence/OTU classification

Day 3:

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


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


Reproducible Research 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 are interested in understanding how to make their analyses more reproducible and easier to distribute to colleagues, advisors, and other scientists. The workshop is an even blend of lecture/discussion and hands on with real data and typically uses mothur output files as a starting point. This is a new workshop that I am offering, so here is a rough outline of what the workshop schedule will look like (it is subject to some minor changes)...

  • Problems with reproducibility
  • Data organization
  • Version control
  • Scripting
  • R-markdown