PHS 7045: Advanced Programming — Fall 2026

Welcome to Advanced Programming in R and HPC! The instructors are George G. Vega Yon, Ph.D. and Thi-Mui Pham, Ph.D..¹ You can find the Fall 2026 syllabus. Readings for each session can be found in the GitHub issues associated with them.

Contents

Week	Date	Session	Title	Materials
1	8/25/26	Lecture	Intro classes AI	slides (source)
1	8/27/26	Lab	How to use AI in the class	slides (source)
2	9/1/26	Lecture	Intro to Git	slides (source)
2	9/3/26	Lab	Git and Github exercises	lab (source) + [quarto](https://UofUEpiBio.github.io/PHS7045-advanced-programming/01-git/quarto.html){target="_blank" rel="noopener"} ([source](01-git/quarto.qmd){target="_blank" rel="noopener"})
2	9/8/26	Lecture	Functional programming	slides (source)
2	9/10/26	Lab	Functional programming	lab (source) + [Homework 2](https://UofUEpiBio.github.io/PHS7045-advanced-programming/04-more-functions-and-datatable/homework.html){target="_blank" rel="noopener"} ([source](04-more-functions-and-datatable/homework.qmd){target="_blank" rel="noopener"})
3	9/15/26	Lecture	Debugging and profiling	slides (source)
3	9/17/26	Lab	Debugging and profiling	lab (source)
4	9/22/26	Lecture	Introduction to C++	slides (source)
4	9/24/26	Lab	Introduction to C++	lab (source)
5	9/29/26	Lecture	C++ in R	slides (source)
5	10/1/26	Lab	C++ in R	lab (source) Deliver a paragraph in abstract mode describing their projects for the midterm.
6	10/6/26	Lecture	Parallel Computing	slides (source)
6	10/8/26	Lab	Parallel Computing	lab (source)
7	10/13/26	Break	Fall Break
7	10/15/26	Break	Fall Break
8	10/20/26	Lecture and Lab	Bonus Track 1: More on AI
8	10/22/26	Lecture and Lab	Bunus Track 2: Ollama
9	10/27/26	Lecture	Midterm project: Hackathon
9	10/29/26	Lab	Midterm project: Presentations (lightning talk)	Homework 3 (source)
10	11/3/26	Lecture and Lab	UofU's CHPC intro	CHPC overview Linux slides, using R slides, Slurm slides
10	11/5/26	Lecture and Lab	UofU's CHPC coding agents	lab (source)
11	11/10/26	Lecture	Slurm	slides (source)
11	11/12/26	Lab	More practice with slurm	slides (source)
12	11/17/26	Lecture	R packages I	slides (source)
12	11/19/26	Lab	R packages I	lab (source)
13	11/24/26	Lecture	TBD
13	11/26/26	Lab	Thanksgiving recess
14	12/1/26	Lecture	Automatic Reports with GitHub Actions	slides (source)
14	12/3/26	Off	TBD (maybe something about agents orchestration or whatnot)
15	12/8/26	Lecture	Final Prep (Hackathon)
15	12/10/26	Lab	Final Prep (Hackathon)
16	12/15/26	Lecture	Final
16	12/17/26	Lecture	Final	Requirements

Assignment workflow

Assignment materials will be distributed in a single compressed file (usually zip) for each assignment. Once the assignment materials are available, the students are required to do the following:

1. Download the compressed file and extract its contents into an empty folder.

2. Initialize the folder as a git repository, add its contents, and make the first commit.

3. Create a new repository in Github.com (under your account) and push your local repo into it. The name of the repository should be [name of the compressed file]-[your GitHub username]

You can start working on your assignment! We recommend pushing your changes as much as possible (it is good practice). As soon as you finish your assignment, you will have to ping one of the instructors in your commit message, for example:

git commit -a -m "Assignment done @gvegayon and @tm-pham"

This way the course instructors, George G. Vega Yon (@gvegayon) and Thi Mui Pham (@tm-pham), will receive a notification about this assignment. Furthermore, we encourage you to use other GitHub resources, such as adding the URL of GitHub issue regarding that assignment, for example, if you include the following link in your commit message:

git commit -a -m "Assignment done https://github.com/UofUEpiBio/PHS7045-advanced-programming/issues/17"

Issue #17 in the PHS7045 website will now include a link to your commit. A similar thing can be done by cross-referencing an issue; this is, if you create a new issue in your repository and include the same link (https://github.com/UofUEpiBio/PM566/issues/17), the issue will be shown in #17 as cross-referenced.

Example

For week #3, we will distribute a zip file named week3-assignment.zip. Using the command line, you can do all the previous steps as follows:

cd ~
wget github.com/UofUEpiBio/PHS7045-advanced-programming/raw/master/assignments/week3-assignment.zip
unzip week3-assignment.zip -d week3-assignment-gvegayon
cd week3-assignment-gvegayon
git init
git add .
git commit -a -m "Initial commit"

You still need to go to Github.com to create the new repository. Assuming you do that successfully, we continue:

git remote add origin git@github.com:gvegayon/week3-assignment-gvegayon.git
git push -u origin master

And you are done!

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1. This course was first offered in Spring 2023 by George G. Vega Yon and Jonathan Chipman.