Lectures

The course covers the following topics, with corresponding lecture materials available in the lectures folder. Please refer to the syllabus for additional suggested readings on each topic. Links will be added as the materials are posted.

Module 01: Introduction

August 27, 2025:

Syllabus and course repository: https://github.com/danilofreire/qtm350.
Lecture 01: Welcome to QTM 350 - Introduction.
Course Tutorials: How to Install Anaconda, Jupyter, PostgreSQL, VSCode, and Open a Free Educational Account on GitHub.

Suggested references:

Cleveland, W. S. (2001). Data science: An action plan for expanding the technical areas of the field of statistics. International Statistical Review, 69(1), 21-26.
Donoho, D. (2017). 50 Years of Data Science. Journal of Computational and Graphical Statistics, 26(4), 745-766.
Breiman, L. (2001). Statistical Modeling: The Two Cultures (with Comments and a Rejoinder by the Author). Statistical Science, 16(3), 199-231.
Brady, H. E. (2019). The Challenge of Big Data and Data Science. Annual Review of Political Science, 22(1), 297-323.
Zitnik, M., Nguyen, F., Wang, B., Leskovec, J., Goldenberg, A., & Hoffman, M. M. (2019). Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. Information Fusion, 50, 71-91.

September 3, 2025:

Lecture 02: Computational Literacy.
Assignment 01: Problem Set 01.

Suggested references:

Campbell-Kelly, M., Aspray, W. F., Yost, J. R., Tinn, H., & Díaz, G. C. (2023). Computer: A History of the Information Machine. Routledge.
Shalf, J. (2020). The Future of Computing beyond Moore’s Law. Philosophical Transactions of the Royal Society A, 378(2166), 20190061.
Al-Hashimi, H. M. (2023). Turing, von Neumann, and The Computational Architecture of Biological Machines. Proceedings of the National Academy of Sciences, 120(25), e2220022120.
Wing, J. M. (2006). Computational Thinking. Communications of the ACM, 49(3), 33-35.
Videos: David J. Malan - Abstraction, Khan Academy - Hexadecimal Number System, Matthias Wandel - Marble Adding Machine, Crash Course - Early Computing and Electronic Computing (the last two are quite entertaining!).

Module 02: Introduction to the Command-Line Interface and Version Control

September 8, 2025:

Lecture 03: The Command-Line Interface (CLI), Shell Basics, and File Management.
Kahoot Quiz

Suggested references:

Janssens, J. (2021). Data Science at the Command Line: Obtain, Scrub, Explore, and Model Data with Unix Power Tools (2nd ed.). O’Reilly Media.
Levy, J. (2024). The Art of Command Line. GitHub.
Shotts, W. (2019). The Linux Command Line: A Complete Introduction. No Starch Press.
Healy, K. (2019). The Plain Person’s Guide to Plain Text Social Science. Chapters 1-5.

September 10, 2025:

Lecture 04: More Command Line Tools, Text Files and Scripting.
Assignment 01 due (5%).
Assignment 02: Problem Set 02.
Kahoot Quiz.

Suggested references:

Kerr, D. (2024). Effective Shell.
Irianto, I. (2021). Learn Vim (the Smart Way).
Neil, D. (2015). Practical Vim: Edit Text at the Speed of Thought. Pragmatic Bookshelf.
Dennis, J. Your problem with Vim is that you don’t grok vi. (Stack Overflow).
Vim Adventures. (Instructor’s note: this is a fun, albeit cringy, way to learn Vim).
Videos: freeCodeCamp - Command line crash course, Percy Grunwald - Absolute beginner guide to the macOS terminal, NetworkChuck - 50 macOS tips and tricks using terminal

September 15, 2025:

Lecture 05: Version control with Git and GitHub.
Kahoot Quiz.

Suggested references:

Chacon, S. and Straub, B. (2014). Pro Git. Apress. (Instructor’s note: this is the book on Git).
GitHub tutorials: GitHub skills (recommended), Git guides, GitHub learning lab, Best practices for repositories.

September 17, 2025:

Lecture 06: More Git and GitHub: pull requests, issues, pages, and collaboration features.
Kahoot Quiz.
Assignment 02 due (5%).
Assignment 03: Problem Set 03.

Suggested references:

Perez-Riverol, Y., Gatto, L., Wang, R., Sachsenberg, T., Uszkoreit, J., Leprevost, F. da V., Fufezan, C., Ternent, T., Eglen, S. J., Katz, D. S., Pollard, T. J., Konovalov, A., Flight, R. M., Blin, K., & Vizcaíno, J. A. (2016). Ten Simple Rules for Taking Advantage of Git and GitHub. PLOS Computational Biology, 12(7), e1004947.
Beckman, M. D., Çetinkaya-Rundel, M., Horton, N. J., Rundel, C. W., Sullivan, A. J., & Tackett, M. (2021). Implementing version control with git and GitHub as a learning objective in statistics and data science courses. Journal of Statistics and Data Science Education, 29(sup1), S132-S144.
Escamilla, E., Klein, M., Cooper, T., Rampin, V., Weigle, M. C., & Nelson, M. L. (2022). The Rise of GitHub in Scholarly Publications. arXiv preprint arXiv:2208.04895.

September 22, 2025:

Lecture 07: Git and GitHub Continued.
Kahoot Quiz.

Module 03: Literate Programming with Markdown, Quarto, and Jupyter

September 24, 2025:

Lecture 08: Quiz 01: Git and Github (6%).
Assignment 03 due (5%).
Assignment 04: Problem Set 04.

Suggested references:

Quarto official website.
Awesome Quarto: https://github.com/mcanouil/awesome-quarto. Note: this repository contains dozens of tutorials, examples, and resources.
Çetinkaya-Rundel, M. & Lowndes, J. S. (2022) Keynote talk: Hello Quarto: Share • Collaborate • Teach • Reimagine. Slides and source code. This is one of the nicest Quarto presentations I have seen.
Getting Started with Quarto (YouTube). Note: Posit (formerly RStudio) has a series of tutorials on Quarto on their YouTube channel. You can find their playlist here.
Markdown Guide.
Jupyter Notebooks Documentation.
Codecademy - How to use Jupyter Notebooks
Course tutorial: Jupyter and Markdown

September 29, 2025:

Lecture 09: Introduction to Quarto.

Suggested references:

Quarto official website.
Awesome Quarto: https://github.com/mcanouil/awesome-quarto. Note: this repository contains dozens of tutorials, examples, and resources.
Çetinkaya-Rundel, M. & Lowndes, J. S. (2022) Keynote talk: Hello Quarto: Share • Collaborate • Teach • Reimagine. Slides and source code. This is one of the nicest Quarto presentations I have seen.
Getting Started with Quarto (YouTube). Note: Posit (formerly RStudio) has a series of tutorials on Quarto on their YouTube channel. You can find their playlist here.