Programming for Biomedical Informatics

Informatics (INFR11260), Semester 1, 2025

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All course materials can be kept up to date by syncing with the course GitHub repository

Week 4 Tasks

Oct 5 · 1 min read

  1. keep practicing with your preferred python coding environment using the notebooks accompanying each week’s work.

  2. have a go at the new week 4 practice assignment in the GitHub Classroom. Remember these are not assessed, they are for you to practice related coding as the course progresses.

  3. I have decided to include the solution for the week3 optional assignment from GitHub Classroom right away this week which we will go through on Thursday

If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in puclic). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.

Remember that I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.

List of Weekly Tasks

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). You will learn about established data formats for different data modalities so that you can understand the structure and content of the data and how it was generated. Each week we will focus on analytical tasks in linked topics that span 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, and biomedical text analysis. Each topic will be explored using real-world examples.

On successful completion of this course, you should be able to:

  1. select sources of biomedical data appropriate for a given research question.
  2. determine the most suitable methods to use to analyse these data.
  3. implement and critically evaluate advanced Python code for biomedical data projects using reproducible research practices.