Syllabus
What the course covers and what you will be able to do
This page summarizes the content. The official CBIO7501 syllabus (credits, grading, deadlines, attendance and academic integrity policies) is the one published by the course and on the course repository’s README; where they differ, the official syllabus applies.
CBIO7501: The Art of Reproducible Research, MBZUAI, Fall 2026. 2 credits; seven weeks; Monday 15:00–16:20, lecture; Tuesday 16:00–17:20, lecture; Wednesday 17:00–18:50, lab. Instructor: Aziz Khan.
Course learning outcomes
By the end of the course you can:
- Explain what makes computational research reproducible, replicable and open, and audit a published study against the five pillars and FAIR.
- Organize a project so that raw data stays untouched, data is downloaded and checked by code, and results can be rebuilt with one command.
- Write reports and notebooks in which every result is computed from the data when they render.
- Use Git and GitHub to record, review and share work, and continuous integration to check it reproduces on a fresh machine.
- Pin and rebuild software environments with Pixi lock files, and package them in containers for laptops and clusters.
- Automate a multi-step analysis with a workflow manager (Snakemake; an introduction to Nextflow), and show that independent implementations agree.
- Document, license, cite and archive a project so that others may and can reuse it.
Topics by week
| Week | Topic | Lessons |
|---|---|---|
| 1 | Introduction to reproducibility and open science | 01, 03 (concepts); slides (PDF): Lecture 1, Reproducibility, Lecture 2, Open science |
| 2 | Project organization and version control: Git and GitHub | 02, 03, 04 (§1–6) |
| 3 | Portable and reproducible environments (Pixi first; Conda compared) | 04 (§7–10), 05, 05b |
| 4 | Literate programming: Jupyter and Quarto | 06, 07 |
| 5 | Containers: Docker and Apptainer | 08 |
| 6 | Workflows and automation: Snakemake and Nextflow | 09, 10 |
| 7 | Publishing, archiving and open science practice | 11, 12 |
How the course works
Hands-on: short slides, then tutorials on one shared example, the LTEE project. From Week 2 you also apply each tool to your own research project, the capstone. Two projects are assessed:
| Project | What it is | Share of the grade | Assessed with |
|---|---|---|---|
| LTEE project | the project you build in the hands-on parts of the lessons, on GitHub, released with a Zenodo DOI | 40% | what to hand in |
| Capstone | your own existing research project (or a manageable part of it), separate from the LTEE project; public, or private and shared with the instructor; no DOI needed | 30% | capstone rubric |
The rest of the grade, the deadlines and the policies are in the official syllabus.
Readings
Each lesson ends with Further reading. The core papers are listed on the Sources and credits page.