About this Course Material

This is a webpage describing the course material I have been developing for HMSP410, Health Informatics. This is a course that is co-taught with Bill Hersh for the OHSU/PSU School of Public Health. They are intended for students with very little math and programming background. Where possible, I’ve tried to have hands-on activities for each of the subjects.

Week 1.2 Introduction to Bioinformatics

This is a brief introduction to genotyping and phenotyping through the lens of Genome Wide Association Studies. In the activity, students are given SNPs to explore using the EBI GWAS browser and we crowdsource our results.

Week 2.2 Introduction to Genomics

In this lecture, we talk about issues with Genotyping in the context of cancer mutations, in particular the idea of depth and coverage. In the activity, students are given paired tumor/normal sequences samples and they need to compare the two sets of sequences to identify a mutation in the KRAS gene. This activity was adapted from yourgenome.org.

Week 4.1 Introduction to Visualization/Data Literacy

In this lecture, we talk about some basic forms of visualization and how to understand them. We go from categorical and continuous data to understanding the relationships between variables. I used shiny and learnR to produce some interactive visualizations that allow students to explore different visualizations.

Parts of this tutorial came from Mikhail Popov’s excellent Data Literacy Tutorial and a LearnR package I did with Jessica Minnier called DSIExplore.

Week 4.2 A Guided Tour through Data Science

This is a guided tour about some of the basic issues in data science. It uses datacamp-light and tutorial along with the tidyverse to show some ways to visualize and manipulate data.

Week 6.1 An Introduction to Ethics

This is a short introduction to ethical decision making and the role informatics can play in it. The in-class group activity is doing a short ethical analysis.