PBI: Programming for Biomedical Informatics

In this course, you will learn:

• how to use Python to retrieve and parse data from biological repositories through bulk download and application programming interfaces (APIs).
• about established data formats for different data modalities so that you understand the structure and content of the data and how it was generated.
• how to perform analytic tasks in linked topics spanning the main components of modern biomedical informatics research. Topics will change slightly each year, but will typically include:
  • tools, algorithms, and approaches for biological sequence, multi-omics (transcriptomics, proteomics, methylomics)
  • biomedical network analysis
  • biomedical text analysis.

Each topic will be explored using real-world examples.

The course will be taught in twice weekly paired lectures, with the first lecture introducing background material, programming concepts, and techniques and the second lecture demonstrating their applied use in an interactive tutorial style. The course will be supported by Jupyter Notebooks for each topic that will contain technical programming examples and exemplars of their application to real-world biomedical data.

Summative assessment will consist of coding problems in each topic area and a final exam based on the lecture and tutorial content.

This year's course will be hosted on GitHub in a new repository here, updated for this year each week.