Teaching and Mentoring Interests

Current Academic Coursework at OHSU and PSU

I teach in the summer hybrid BMI569/669 Data Analytics course at OHSU (Hybrid course co-taught with Kaiser Permanente Data & Information Management Enhancement (DIME) group).

I am also a co-instructor for BMI551/651 Bioinformatics and Computational Biology II: Statistical Methods, providing drop-in sessions for R programming and general tutoring.

We are teaching an introductory bootcamp in python called NEU640 Python Bootcamp for Neuroscientists.. This is a week-long course meant to introduce neuroscience students to the basics of python with data types familiar to them, including imaging and electrophysiology data. Taught with Stephen David, Brad Buran, Daniela Sadieri, Lucille Moore, Charlie Heller, Zack Schwartz. Winter Quarter, 2018.

I am course co-director for HSMP/PHE410 Introduction to Health Informatics. at Portland State University. Spring Quarter, 2018.

DataCamp

I have a free online introductory course at DataCamp called the RBootcamp. In this course, we cover the basics of visualization, data munging, and basic statistics using the tidyverse in R. It is freely available to everyone, but registration is required.

I am currently developing a course called Statistical Analysis of Networks in R for DataCamp. More info as it develops.

Training Materials/Workshops

I have developed a number of self-directed training materials for learning R and specific packages that I’ve found useful. Most of these are available from my github page and may be used freely by students.

  • R-Bootcamp (tidyverse) - The new version of RBootcamp, that covers the tidyverse for manipulating data in R. You will need to register on DataCamp. This interactive course was written with both Jessica Minnier and Chester Ismay. DOI
  • R-Bootcamp (Base R) - an MOOC (Massively Open Online Course) for teaching the basics of data manipulation in R (Coursesites registration required). Note that I do not support this course anymore at this point.

Standalone Tutorials

Many of these tutorials have been given through the student club at OHSU that I mentor, called BioData Club. They are all freely available to be reused by other instructors.

  • The Magic of Markdown - An introduction to the many uses of Markdown, including RMarkdown for reproducible scripting.
  • GitHub Pages - A pain free introduction to getting a personal website started using GitHub pages. With Robin Champieux and Eric Leung.

R Tutorials

As a developer and programmer of R, I enjoy teaching others about the basics of data wrangling and analysis. Here are a few of the tutorials I’ve put together.

Big Data to Knowledge

As an instructor under OHSU’s Big Data To Knowledge (BD2K) Training Grant, I have also developed the following short workshops to encourage students to explore data and learn the basics of data-wrangling.

Other Teaching Interests

  • BioData Club - A student and postdoc driven discussion group at OHSU that focuses on practical skills (documentation, software engineering and visualization) necessary for success in data science and bioinformatics.
  • I participate in the PDX R User Group and I was one of the organizers of the first Cascadia R conference
  • I have also started to contribute lesson material to Software Carpentry.